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Changes between Initial Version and Version 1 of Ticket #17360

Timestamp:: Apr 14, 2025, 10:38:23 AM (6 months ago)
Author:: pett
Comment:

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #17360
- Property Component Unassigned → Input/Output
- Property Owner set to Tom Goddard
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → assigned
- Property Summary ChimeraX bug report submission → MOLE JSON: atom radius must be positive

Ticket #17360 – Description

-              initial
+              v1
 atoms, 304 bonds, 38 residues, 1 model selected
+> select #1/B:147-186
+atoms, 320 bonds, 40 residues, 1 model selected
+> select #1/C:148-185
+atoms, 304 bonds, 38 residues, 1 model selected
+> select #1/B:147-186
+atoms, 320 bonds, 40 residues, 1 model selected
+> select #1/B:147-186 & #1/C:148-185
+Nothing selected
+> select #1/B:147-186 & /C:148-185
+Nothing selected
+> select #1/B:147-186, C:148-185
+atoms, 320 bonds, 40 residues, 1 model selected
+> select #1/B:147-186, #1/C:148-185
+Expected an objects specifier or a keyword
+> select add #1
+atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
+> select subtract #1
+Nothing selected
+> select add #1
+atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
+> show #!3 models
+> ~select
+Nothing selected
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> matchmaker #1/E to #3/E
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain E (#3) with
+MolBC_chains_renamed.pdb, chain E (#1), sequence alignment score = 1188
+RMSD between 242 pruned atom pairs is 0.927 angstroms; (across all 244 pairs:
+.967)
+> ~select
+Nothing selected
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> ~SEL
+Unknown command: ~SEL
+> ~select
+Nothing selected
+> matchmaker #1/B:147-186 to #3/B:149-186
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
+MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 189.9
+RMSD between 38 pruned atom pairs is 0.500 angstroms; (across all 38 pairs:
+.500)
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> select
+atoms, 25916 bonds, 25 pseudobonds, 3985 residues, 7 models selected
+> ~select
+Nothing selected
+> matchmaker #1/C:148-185 to #3/C:147-185
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
+MolBC_chains_renamed.pdb, chain C (#1), sequence alignment score = 189.2
+RMSD between 38 pruned atom pairs is 0.592 angstroms; (across all 38 pairs:
+.592)
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> ~select
+Nothing selected
+> ui mousemode right select
+Drag select of 409 residues, 4 pseudobonds
+> ~select
+Nothing selected
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> select
+atoms, 25916 bonds, 25 pseudobonds, 3985 residues, 7 models selected
+> matchmaker
+Missing or invalid "matchAtoms" argument: empty atom specifier
+> ~select
+Nothing selected
+> align
+Missing or invalid "atoms" argument: empty atom specifier
+> ui tool show Matchmaker
+> matchmaker #!3 & sel to #1 & sel showAlignment true
+No 'to' model specified
+> matchmaker #!3 & sel to #1 & sel showAlignment true
+No 'to' model specified
+> matchmaker #!3 to #1 showAlignment true
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolBC_chains_renamed.pdb, chain B (#1) with
+MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
+score = 1451.5
+Alignment identifier is 1
+Showing conservation header ("seq_conservation" residue attribute) for
+alignment 1
+Hiding conservation header for alignment 1
+Chains used in RMSD evaluation for alignment 1: MolBC_chains_renamed.pdb #1/B,
+MolBC_WT_final_structure_chains_renamed.pdb #3/B
+Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
+RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
+.077)
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> ~select
+Nothing selected
+> select TM5_5a_crystal
+Nothing selected
+> hide #!3 models
+> select #1/B:147
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/B:147-150
+atoms, 31 bonds, 4 residues, 1 model selected
+> select #1/B:147
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/B:147-186
+atoms, 320 bonds, 40 residues, 1 model selected
+> ui mousemode right select
+> select #1/C:148-185
+atoms, 304 bonds, 38 residues, 1 model selected
+> select #1/C:147
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/C:5-147
+atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> select #1/C:171-172
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #1/C:171-330
+atoms, 1257 bonds, 160 residues, 1 model selected
+> cartoon hide sel
+> select #1/B:146
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #1/B:6-146
+atoms, 956 bonds, 2 pseudobonds, 124 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> select #1/B:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/B:171-330
+atoms, 1257 bonds, 160 residues, 1 model selected
+> cartoon hide sel
+Drag select of 47 residues
+> select up
+atoms, 2888 bonds, 369 residues, 1 model selected
+> select up
+atoms, 2913 bonds, 372 residues, 1 model selected
+> select up
+atoms, 4226 bonds, 546 residues, 1 model selected
+> select up
+atoms, 4375 bonds, 565 residues, 1 model selected
+> select up
+atoms, 4703 bonds, 608 residues, 1 model selected
+> select down
+atoms, 4375 bonds, 565 residues, 1 model selected
+> select down
+atoms, 4226 bonds, 546 residues, 1 model selected
+> select down
+atoms, 2913 bonds, 372 residues, 1 model selected
+> select down
+atoms, 2888 bonds, 369 residues, 1 model selected
+> select down
+atoms, 47 residues, 1 model selected
+> select down
+atoms, 47 residues, 1 model selected
+> select down
+atoms, 47 residues, 1 model selected
+> select down
+atoms, 47 residues, 1 model selected
+> ~select
+Nothing selected
+Drag select of 47 residues
+> select down
+atoms, 47 residues, 1 model selected
+> select up
+atoms, 2888 bonds, 369 residues, 1 model selected
+> select down
+atoms, 47 residues, 1 model selected
+> ~select
+Nothing selected
+Drag select of 47 residues
+> name 5_5a_crystal #1/sel
+Not registering illegal selector name "5_5a_crystal"
+> name TM5_5a_crystal_real #1/sel
+> ~select
+Nothing selected
+> select TM5_5a_crystal_real
+Nothing selected
+Drag select of 47 residues
+> name TM5_5a_crystal_real #1
+> ~select
+Nothing selected
+> select TM5_5a_crystal_real
+atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
+> ~select
+Nothing selected
+> show #!3 models
+> select #3/C:146
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #3/C:7-146
+atoms, 857 bonds, 2 pseudobonds, 112 residues, 2 models selected
+> cartoon hide (#!3 & sel)
+> select #3/C:186-187
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #3/C:186-328
+atoms, 1111 bonds, 143 residues, 1 model selected
+> cartoon hide sel
+> select #3/C:172
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #3/C:172-185
+atoms, 120 bonds, 14 residues, 1 model selected
+> cartoon hide sel
+> select #3/B:148
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/B:6-148
+atoms, 965 bonds, 2 pseudobonds, 124 residues, 2 models selected
+> cartoon hide (#!3 & sel)
+> select #3/B:171-172
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #3/B:172-328
+atoms, 1232 bonds, 157 residues, 1 model selected
+> cartoon hide sel
+> ui tool show Matchmaker
+> select add #3
+atoms, 8591 bonds, 20 pseudobonds, 1084 residues, 3 models selected
+> select subtract #3
+Nothing selected
+> matchmaker #1/B,C:147-186 to #3/B,C:147-186
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
+MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 195.5
+RMSD between 40 pruned atom pairs is 0.574 angstroms; (across all 40 pairs:
+.574)
+> matchmaker #1/B:147-186 to #3/B:149-186
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
+MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 189.9
+RMSD between 38 pruned atom pairs is 0.500 angstroms; (across all 38 pairs:
+.500)
+> ui mousemode right "translate selected models"
+> select #1/D,E
+atoms, 4040 bonds, 1 pseudobond, 877 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> select #3/D,E
+atoms, 3935 bonds, 4 pseudobonds, 486 residues, 2 models selected
+> cartoon hide (#!3 & sel)
+> select add #3
+atoms, 8591 bonds, 20 pseudobonds, 1084 residues, 3 models selected
+> select subtract #3
+Nothing selected
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> ~select
+Nothing selected
+> ui mousemode right zoom
+> hide #!3 models
+> show #!3 models
+> hide #!1 models
+> distance #3/B:172@ca #3/C:172@ca
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B SER 172 CA
+and /C SER 172 CA: 18.960Å
+> show #!4 models
+> show #4.1 models
+> show #!1 models
+> hide #!4 models
+> hide #4.1 models
+> cartoon #1,3
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> movie record
+> turn y 2 180
+> wait 180
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie1.mp4
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie1.mp4
+> hide #!1 models
+> show #!4 models
+> show #4.1 models
+> select #3/C:146
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #3/C:7-146
+atoms, 857 bonds, 2 pseudobonds, 112 residues, 2 models selected
+> cartoon hide (#!3 & sel)
+> select #3/C:172
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #3/C:172-328
+atoms, 1232 bonds, 157 residues, 1 model selected
+> cartoon hide sel
+> select #3/B:328
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #3/B:172-328
+atoms, 1232 bonds, 157 residues, 1 model selected
+> cartoon hide sel
+> select #3/B:148
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/B:6-148
+atoms, 965 bonds, 2 pseudobonds, 124 residues, 2 models selected
+> cartoon hide (#!3 & sel)
+> select #3/D,E
+atoms, 3935 bonds, 4 pseudobonds, 486 residues, 2 models selected
+> cartoon hide (#!3 & sel)
+> select add #3
+atoms, 8591 bonds, 21 pseudobonds, 1084 residues, 3 models selected
+> select subtract #3
+Nothing selected
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> hide #!4 models
+> hide #4.1 models
+> hide #!3 models
+> show #!1 models
+> select #1/C:329-330
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #1/C:171-330
+atoms, 1257 bonds, 160 residues, 1 model selected
+> cartoon hide sel
+> select #1/C:147
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/C:5-147
+atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> select #1/B:330
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/B:171-330
+atoms, 1257 bonds, 160 residues, 1 model selected
+> cartoon hide sel
+> select #1/B:146
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #1/B:6-146
+atoms, 956 bonds, 2 pseudobonds, 124 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> select #1/D,E
+atoms, 4040 bonds, 1 pseudobond, 877 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> select add #1
+atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
+> select subtract #1
+Nothing selected
+> show #!3 models
+> hide #!3 models
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> ~select
+Nothing selected
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> color (#!1 & sel) blue
+> select #1/C
+atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
+> color (#!1 & sel) cornflower blue
+> ~select
+Nothing selected
+> distance #1/B:171@ca #1/C:171@ca
+Distance between MolBC_chains_renamed.pdb #1/B ILE 171 CA and /C ILE 171 CA:
+.605Å
+> show #!4 models
+> show #4.1 models
+> hide #4.1 models
+> hide #!4 models
+> show #!3 models
+> show #!4 models
+> show #4.1 models
+> hide #!4 models
+> hide #4.1 models
+> distance #1/B:171@ca #1/C:171@ca color black
+Distance already exists; modify distance properties with 'distance style'
+> distance #1/B:171@ca #1/C:171@ca color yellow
+Distance already exists; modify distance properties with 'distance style'
+> distance style
+> ui tool show Distances
+Exactly two atoms must be selected!
+> ~distance #1/B:171@CA #1/C:171@CA
+Exactly two atoms must be selected!
+> distance #1/B:171@ca #1/C:171@ca color yellow
+Distance between MolBC_chains_renamed.pdb #1/B ILE 171 CA and /C ILE 171 CA:
+.605Å
+> show distance
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> close #4
+> distance #1/B:171@ca #1/C:171@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B ILE 171 CA and /C ILE 171 CA:
+.605Å
+> hide #!3 models
+> select add #4
+pseudobond, 2 models selected
+> select subtract #4
+Nothing selected
+> view
+> ui tool show Distances
+Exactly two atoms must be selected!
+> select
+> #1/C:6-26,58-60,63-86,99-112,117-137,148-170,177-185,194-214,217-222,225-230,235-256,267-275,279-304,311-327
+atoms, 1695 bonds, 222 residues, 1 model selected
+> select #1/C:5-147
+atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
+> select #1/C:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/C:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> ui mousemode right select
+> select #1/B:170
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #1/B:170
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #1/C:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> cartoon sel
+> select #1/B:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/B:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> cartoon sel
+> ~select
+Nothing selected
+> distance #1/B:169@ca #1/C:169@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B GLN 169 CA and /C GLN 169 CA:
+.324Å
+> distance #1/B:167@ca #1/C:167@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B LEU 167 CA and /C LEU 167 CA:
+.854Å
+> distance #1/B:165@ca #1/C:165@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B VAL 165 CA and /C VAL 165 CA:
+.548Å
+> distance #1/B:163@ca #1/C:163@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B ALA 163 CA and /C ALA 163 CA:
+.665Å
+> distance #1/B:161@ca #1/C:161@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B PHE 161 CA and /C PHE 161 CA:
+.059Å
+> distance #1/B:159@ca #1/C:159@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B GLY 159 CA and /C GLY 159 CA:
+.961Å
+> distance #1/B:157@ca #1/C:157@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B LEU 157 CA and /C LEU 157 CA:
+.684Å
+> distance #1/B:155@ca #1/C:155@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B MET 155 CA and /C MET 155 CA:
+.572Å
+> distance #1/B:153@ca #1/C:153@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B ILE 153 CA and /C ILE 153 CA:
+.521Å
+> distance #1/B:151@ca #1/C:151@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B ILE 151 CA and /C ILE 151 CA:
+.659Å
+> distance #1/B:149@ca #1/C:149@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B MET 149 CA and /C MET 149 CA:
+.266Å
+> label height 1.5
+[Repeated 1 time(s)]
+> ui mousemode right "move label"
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> hide #!4 models
+> hide #4.1 models
+> show #!3 models
+> color #1 #929292ff
+> ui mousemode right zoom
+> cartoon #1,3
+> ui mousemode right "translate selected models"
+> morph
+Missing or invalid "structures" argument: empty atom specifier
+> morph #3,1 frames 40
+Computed 41 frame morph #5
+> coordset #5 1,41
+> morph #3,1 frames 60
+Computed 61 frame morph #6
+> coordset #6 1,61
+> hide #!5 models
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
+> close #5
+> hide #!6 models
+> hide #4.1 models
+> show #!1 models
+> show #!3 models
+> matchmaker #1/D to #3/D
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain D (#3) with
+MolBC_chains_renamed.pdb, chain D (#1), sequence alignment score = 1119.7
+RMSD between 236 pruned atom pairs is 0.864 angstroms; (across all 238 pairs:
+.082)
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> ~select
+Nothing selected
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> movie record
+> turn y 2 180
+> wait 180
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie1.mp4
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie1.mp4
+> hide #!1 models
+> select #3/B,C
+atoms, 4656 bonds, 4 pseudobonds, 598 residues, 2 models selected
+> cartoon hide (#!3 & sel)
+> select #3/D,E
+atoms, 3935 bonds, 4 pseudobonds, 486 residues, 2 models selected
+Alignment identifier is 3/D
+Alignment identifier is 3/E
+> select add #3
+atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
+> select subtract #3
+Nothing selected
+> ui mousemode right zoom
+> view
+> select #3/D:38-39
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #3/D:38-53
+atoms, 89 bonds, 1 pseudobond, 13 residues, 2 models selected
+> ~select
+Nothing selected
+> select #3/D:45
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #3/D:45
+atoms, 5 bonds, 1 residue, 1 model selected
+> ~select
+Nothing selected
+> select #3/D:129
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/D:129-133
+atoms, 30 bonds, 5 residues, 1 model selected
+> select #3/D:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/D:129-133
+atoms, 30 bonds, 5 residues, 1 model selected
+> select #3/E:129
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/E:129-133
+atoms, 30 bonds, 5 residues, 1 model selected
+> select add #3
+atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
+> select subtract #3
+Nothing selected
+> distance #3/D:45@ca #3/E:133@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/D SER 45 CA
+and /E GLN 133 CA: 23.027Å
+> show #4.1 models
+> label height 1.5
+> label height 2
+> label height 4
+> label height 3
+[Repeated 1 time(s)]
+> ui mousemode right "move label"
+> select #3/D:45
+atoms, 5 bonds, 1 residue, 1 model selected
+> color sel black
+> select #3/e:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel black
+> ui mousemode right zoom
+> select add #3
+atoms, 8591 bonds, 9 pseudobonds, 1084 residues, 3 models selected
+> select subtract #3
+Nothing selected
+> ui mousemode right "move label"
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> hide #!3 models
+> show #!1 models
+> hide #!4 models
+> hide #4.1 models
+> select #1/B,C
+atoms, 4703 bonds, 16 pseudobonds, 912 residues, 3 models selected
+> cartoon hide (#!1 & sel)
+> select #1/d
+atoms, 2035 bonds, 421 residues, 1 model selected
+> color sel purple
+> select #1/e
+atoms, 2005 bonds, 1 pseudobond, 456 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel violet
+> ~select
+Nothing selected
+> distance #1/D:45@ca #1/E:133@ca color black
+Distance between MolBC_chains_renamed.pdb #1/D SER 45 CA and /E GLN 133 CA:
+.019Å
+> show #!4 models
+> show #4.1 models
+> label height 3
+[Repeated 1 time(s)]
+> select #1/e:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel black
+> select #1/d:45
+atoms, 5 bonds, 1 residue, 1 model selected
+> color sel black
+> ~select
+Nothing selected
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> hide #4.1 models
+> hide #!4 models
+> color #1 #929292ff
+> hide #!1 models
+> show #!3 models
+> cartoon #3
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> select #3/d
+atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
+> color (#!3 & sel) purple
+> select #3/e
+atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel violet
+> ~select
+Nothing selected
+> select #3
+atoms, 8591 bonds, 9 pseudobonds, 1084 residues, 3 models selected
+> show sel surfaces
+> hide sel cartoons
+> select add #4
+atoms, 8591 bonds, 22 pseudobonds, 1084 residues, 8 models selected
+> select subtract #4
+atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 6 models selected
+> ~select
+Nothing selected
+> ui mousemode right zoom
+> ui tool show "Side View"
+> hide #!3 models
+> show #!1 models
+> cartoon #1
+> select #1/B
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> color (#!1 & sel) blue
+> select #1/c
+atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
+> color (#!1 & sel) cornflower blue
+> select #1/d
+atoms, 2035 bonds, 421 residues, 1 model selected
+> color sel purple
+> select #1/e
+atoms, 2005 bonds, 1 pseudobond, 456 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel violet
+> select #1
+atoms, 8743 bonds, 18 pseudobonds, 1789 residues, 3 models selected
+> show sel surfaces
+> hide sel cartoons
+> ~select
+Nothing selected
+> hide #!1 models
+> show #!3 models
+> transparency #3 50
+> transparency #3 70
+> select #3/B,C
+atoms, 4656 bonds, 4 pseudobonds, 598 residues, 2 models selected
+Alignment identifier is 3/B
+Alignment identifier is 3/C
+> ~select
+Nothing selected
+> select #3/B:149
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/B:149-171
+atoms, 175 bonds, 23 residues, 1 model selected
+> show sel cartoons
+> select #3/C:147
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/C:147-171
+atoms, 191 bonds, 25 residues, 1 model selected
+> show sel cartoons
+> ~select
+Nothing selected
+> distance #3/B:171@ca #3/C:171@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ILE 171 CA
+and /C ILE 171 CA: 23.254Å
+> show #!4 models
+> show #4.1 models
+> distance #3/B:169@ca #3/C:169@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B GLN 169 CA
+and /C GLN 169 CA: 15.005Å
+> distance #3/B:167@ca #3/C:167@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B LEU 167 CA
+and /C LEU 167 CA: 22.657Å
+> distance #3/B:165@ca #3/C:165@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B VAL 165 CA
+and /C VAL 165 CA: 18.432Å
+> distance #3/B:163@ca #3/C:163@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ALA 163 CA
+and /C ALA 163 CA: 20.352Å
+> distance #3/B:161@ca #3/C:161@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B PHE 161 CA
+and /C PHE 161 CA: 22.692Å
+> distance #3/B:159@ca #3/C:159@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B GLY 159 CA
+and /C GLY 159 CA: 18.050Å
+> distance #3/B:157@ca #3/C:157@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B LEU 157 CA
+and /C LEU 157 CA: 25.168Å
+> distance #3/B:155@ca #3/C:155@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B MET 155 CA
+and /C MET 155 CA: 16.815Å
+> distance #3/B:153@ca #3/C:153@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ILE 153 CA
+and /C ILE 153 CA: 26.245Å
+> distance #3/B:151@ca #3/C:151@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ILE 151 CA
+and /C ILE 151 CA: 18.493Å
+> distance #3/B:149@ca #3/C:149@ca color black
+Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B MET 149 CA
+and /C MET 149 CA: 25.488Å
+> label height 3
+> label height 1.5
+[Repeated 1 time(s)]
+> transparency #3-4 0
+> transparency #3-4 60
+> label height 2.5
+> label height 2
+> ui mousemode right label
+[Repeated 1 time(s)]
+> ui mousemode right zoom
+> ui mousemode right "move label"
+> ui tool show Distances
+[Repeated 1 time(s)]
+> distance style symbol false
+[Repeated 2 time(s)]
+> distance style symbol true
+[Repeated 2 time(s)]
+> select add #4
+pseudobonds, 2 models selected
+> select subtract #4
+Nothing selected
+> select add #4.1
+model selected
+> select add #4
+pseudobonds, 2 models selected
+> select subtract #4
+Nothing selected
+> ui mousemode right select
+> select #3/D:246@CD
+atom, 1 residue, 1 model selected
+> select #3/D:246@CD
+atom, 1 residue, 1 model selected
+> ~select
+Nothing selected
+> ui tool show Distances
+> ~distance #3/B:149@CA #3/C:149@CA
+> ui mousemode right "move label"
+> ~distance #3/B:151@CA #3/C:151@CA
+> ~distance #3/B:153@CA #3/C:153@CA
+> ~distance #3/B:155@CA #3/C:155@CA
+> ~distance #3/B:157@CA #3/C:157@CA
+> ~distance #3/B:159@CA #3/C:159@CA
+> ~distance #3/B:161@CA #3/C:161@CA
+> ~distance #3/B:163@CA #3/C:163@CA
+> ~distance #3/B:165@CA #3/C:165@CA
+> ~distance #3/B:167@CA #3/C:167@CA
+> ~distance #3/B:169@CA #3/C:169@CA
+> ~distance #3/B:171@CA #3/C:171@CA
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> hide #!3 models
+> show #!1 models
+> transparency #1,4 60
+> select #1/b,c
+atoms, 4703 bonds, 16 pseudobonds, 912 residues, 3 models selected
+Alignment identifier is 1/B
+Alignment identifier is 1/C
+> ~select
+Nothing selected
+> select #1/B:147-148
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #1/B:147-170
+atoms, 183 bonds, 24 residues, 1 model selected
+> show sel cartoons
+> select #1/C:148
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/C:148-170
+atoms, 175 bonds, 23 residues, 1 model selected
+> show sel cartoons
+> ~select
+Nothing selected
+> ui mousemode right "move label"
+> color #4 black models
+> ui tool show Distances
+> ~distance #1/B:149@CA #1/C:149@CA
+> distance #1/B:149@ca #1/C:149@ca color black
+Distance between MolBC_chains_renamed.pdb #1/B MET 149 CA and /C MET 149 CA:
+.266Å
+> label height 2
+> ~distance #1/B:149@CA #1/C:149@CA
+> ~distance #1/B:151@CA #1/C:151@CA
+> ~distance #1/B:153@CA #1/C:153@CA
+> ~distance #1/B:155@CA #1/C:155@CA
+> ~distance #1/B:157@CA #1/C:157@CA
+> ~distance #1/B:159@CA #1/C:159@CA
+> ~distance #1/B:161@CA #1/C:161@CA
+> ~distance #1/B:163@CA #1/C:163@CA
+> ~distance #1/B:165@CA #1/C:165@CA
+> ~distance #1/B:167@CA #1/C:167@CA
+> ~distance #1/B:169@CA #1/C:169@CA
+> select #1/b,c
+atoms, 4703 bonds, 5 pseudobonds, 912 residues, 3 models selected
+Alignment identifier is 1/B
+Alignment identifier is 1/C
+> ~select
+Nothing selected
+> select #1/B:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/B:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> select #1/C:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/C:171
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> ~select
+Nothing selected
+> ~distance #1/B:171@CA #1/C:171@CA
+> hide #!1 models
+> hide #!4 models
+> hide #4.1 models
+> open
+> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_C5_chains_renamed.pdb
+Chain information for MolBC_WT_in_C5_chains_renamed.pdb #5
+---
+Chain | Description
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+> view
+> select add #5
+atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #5,0.79745,-0.20301,0.56821,-3.4231,-0.56888,-0.56685,0.59586,7.3685,0.20113,-0.79841,-0.56752,20.438
+> ui mousemode right zoom
+> select #5/B
+atoms, 2405 bonds, 2 pseudobonds, 309 residues, 2 models selected
+> color (#!5 & sel) blue
+> select #5/c
+atoms, 2353 bonds, 2 pseudobonds, 303 residues, 2 models selected
+> color (#!5 & sel) cornflower blue
+> select #5/d
+atoms, 2036 bonds, 251 residues, 1 model selected
+> color sel purple
+> select #5/e
+atoms, 2044 bonds, 252 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel violet
+> select add #5
+atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
+> select subtract #5
+Nothing selected
+> select #5/b,c
+atoms, 4758 bonds, 4 pseudobonds, 612 residues, 2 models selected
+Alignment identifier is 5/B
+Alignment identifier is 5/C
+> ~select
+Nothing selected
+> select #5/B:146
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #5/B:4-146
+atoms, 962 bonds, 2 pseudobonds, 125 residues, 2 models selected
+> cartoon hide (#!5 & sel)
+> select #5/B:172
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #5/B:172-330
+atoms, 1250 bonds, 159 residues, 1 model selected
+> cartoon hide sel
+> select #5/C:146
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #5/C:5-146
+atoms, 910 bonds, 2 pseudobonds, 119 residues, 2 models selected
+> cartoon hide (#!5 & sel)
+> select #5/C:172
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #5/C:172-330
+atoms, 1250 bonds, 159 residues, 1 model selected
+> cartoon hide sel
+> hide sel atoms
+> select #5/d,e
+atoms, 4080 bonds, 503 residues, 1 model selected
+> cartoon hide sel
+> ui mousemode right select
+> select clear
+Drag select of 34 atoms, 36 bonds
+> hide sel atoms
+> select add #5
+atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
+> select subtract #5
+Nothing selected
+> select add #5
+atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
+> select subtract #5
+Nothing selected
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> distance #5/B:149@ca #5/C:149@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B MET 149 CA and /C MET
+CA: 24.861Å
+> show #!4 models
+> show #4.1 models
+> distance #5/B:151@ca #5/C:151@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B ILE 151 CA and /C ILE
+CA: 18.415Å
+> distance #5/B:153@ca #5/C:153@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B ILE 153 CA and /C ILE
+CA: 25.604Å
+> distance #5/B:155@ca #5/C:155@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B MET 155 CA and /C MET
+CA: 16.498Å
+> distance #5/B:157@ca #5/C:157@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B LEU 157 CA and /C LEU
+CA: 24.517Å
+> distance #5/B:159@ca #5/C:159@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B GLY 159 CA and /C GLY
+CA: 17.616Å
+> distance #5/B:161@ca #5/C:161@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B PHE 161 CA and /C PHE
+CA: 21.963Å
+> distance #5/B:163@ca #5/C:163@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B ALA 163 CA and /C ALA
+CA: 19.560Å
+> distance #5/B:165@ca #5/C:165@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B VAL 165 CA and /C VAL
+CA: 17.433Å
+> distance #5/B:167@ca #5/C:167@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B LEU 167 CA and /C LEU
+CA: 21.738Å
+> distance #5/B:169@ca #5/C:169@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B GLN 169 CA and /C GLN
+CA: 13.848Å
+> distance #5/B:171@ca #5/C:171@ca color black
+Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B ILE 171 CA and /C ILE
+CA: 22.420Å
+> label height 2
+> label height 1.5
+[Repeated 1 time(s)]
+> ui mousemode right "move label"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> hide #!4 models
+> show #!4 models
+> surface #4-5
+> transparency #4-5 60
+> ui mousemode right "translate selected models"
+[Repeated 1 time(s)]
+> view
+> ui mousemode right "rotate selected models"
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> label height 3
+> label height 2.5
+[Repeated 1 time(s)]
+> ui mousemode right "move label"
+> ~distance #5/B:149@CA #5/C:149@CA
+> ~distance #5/B:151@CA #5/C:151@CA
+> ~distance #5/B:153@CA #5/C:153@CA
+> ~distance #5/B:155@CA #5/C:155@CA
+> ~distance #5/B:157@CA #5/C:157@CA
+> ~distance #5/B:159@CA #5/C:159@CA
+> ~distance #5/B:161@CA #5/C:161@CA
+> ~distance #5/B:163@CA #5/C:163@CA
+> ~distance #5/B:165@CA #5/C:165@CA
+> ~distance #5/B:167@CA #5/C:167@CA
+> ~distance #5/B:169@CA #5/C:169@CA
+> ~distance #5/B:171@CA #5/C:171@CA
+> hide #!5 models
+> open
+> /Users/alexandrakaragiaridi/Desktop/MolABC_no_nuc_everything/MolABC_no_nuc.pdb
+Chain information for MolABC_no_nuc.pdb #7
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+> view
+> select #7/B:6-325
+atoms, 2496 bonds, 320 residues, 1 model selected
+> show sel cartoons
+> hide sel atoms
+> select #7
+atoms, 11571 bonds, 1 pseudobond, 1452 residues, 2 models selected
+> show sel cartoons
+> hide sel atoms
+> select #7/a
+atoms, 2532 bonds, 1 pseudobond, 313 residues, 2 models selected
+> color (#!7 & sel) orange
+> color (#!7 & sel) yellow
+> select #7/b
+atoms, 2496 bonds, 320 residues, 1 model selected
+> color sel blue
+> select #7/c
+atoms, 2465 bonds, 316 residues, 1 model selected
+> color sel cornflower blue
+> select #7/d
+atoms, 2043 bonds, 252 residues, 1 model selected
+> color sel purple
+> select #7/e
+atoms, 2035 bonds, 251 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel violet
+> ui mousemode right zoom
+> select add #7
+atoms, 11571 bonds, 1 pseudobond, 1452 residues, 2 models selected
+> ~select
+Nothing selected
+> select #7/a,d,e
+atoms, 6610 bonds, 1 pseudobond, 816 residues, 2 models selected
+> cartoon hide (#!7 & sel)
+> select #7/b,c
+atoms, 4961 bonds, 636 residues, 1 model selected
+Alignment identifier is 7/B
+Alignment identifier is 7/C
+> ~select
+Nothing selected
+> select #7/B:62
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #7/B:62-87
+atoms, 185 bonds, 26 residues, 1 model selected
+> ~select
+Nothing selected
+> select #7/B:146
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #7/B:6-146
+atoms, 1099 bonds, 141 residues, 1 model selected
+> cartoon hide sel
+> select #7/B:172
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #7/B:172-325
+atoms, 1204 bonds, 154 residues, 1 model selected
+> cartoon hide sel
+> select #7/C:148
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #7/C:6-148
+atoms, 1115 bonds, 143 residues, 1 model selected
+> cartoon hide sel
+> select #7/C:172
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #7/C:172-321
+atoms, 1173 bonds, 150 residues, 1 model selected
+> cartoon hide sel
+> ui mousemode right "translate selected models"
+> view matrix models #7,1,0,0,-0.46625,0,1,0,0.10077,0,0,1,11.839
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> view matrix models #7,1,0,0,0.78501,0,1,0,-0.25841,0,0,1,8.9345
+> distance #7/B:171@ca #7/C:171@ca color black
+Distance between MolABC_no_nuc.pdb #7/B ILE 171 CA and /C ILE 171 CA: 23.719Å
+> distance #7/B:169@ca #7/C:169@ca color black
+Distance between MolABC_no_nuc.pdb #7/B GLN 169 CA and /C GLN 169 CA: 15.265Å
+> distance #7/B:167@ca #7/C:167@ca color black
+Distance between MolABC_no_nuc.pdb #7/B LEU 167 CA and /C LEU 167 CA: 22.879Å
+> distance #7/B:165@ca #7/C:165@ca color black
+Distance between MolABC_no_nuc.pdb #7/B VAL 165 CA and /C VAL 165 CA: 18.972Å
+> distance #7/B:163@ca #7/C:163@ca color black
+Distance between MolABC_no_nuc.pdb #7/B ALA 163 CA and /C ALA 163 CA: 20.705Å
+> distance #7/B:161@ca #7/C:161@ca color black
+Distance between MolABC_no_nuc.pdb #7/B PHE 161 CA and /C PHE 161 CA: 23.247Å
+> distance #7/B:159@ca #7/C:159@ca color black
+Distance between MolABC_no_nuc.pdb #7/B GLY 159 CA and /C GLY 159 CA: 18.386Å
+> distance #7/B:157@ca #7/C:157@ca color black
+Distance between MolABC_no_nuc.pdb #7/B LEU 157 CA and /C LEU 157 CA: 25.664Å
+> distance #7/B:155@ca #7/C:155@ca color black
+Distance between MolABC_no_nuc.pdb #7/B MET 155 CA and /C MET 155 CA: 17.226Å
+> distance #7/B:153@ca #7/C:153@ca color black
+Distance between MolABC_no_nuc.pdb #7/B ILE 153 CA and /C ILE 153 CA: 26.547Å
+> distance #7/B:151@ca #7/C:151@ca color black
+Distance between MolABC_no_nuc.pdb #7/B ILE 151 CA and /C ILE 151 CA: 18.605Å
+> distance #7/B:149@ca #7/C:149@ca color black
+Distance between MolABC_no_nuc.pdb #7/B MET 149 CA and /C MET 149 CA: 25.434Å
+> label height 1.5
+[Repeated 1 time(s)]
+> ui mousemode right "move label"
+> ui mousemode right zoom
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> select add #7
+atoms, 11571 bonds, 13 pseudobonds, 1452 residues, 3 models selected
+> select subtract #7
+Nothing selected
+> select #7/B:172
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #7/B:172-325
+atoms, 1204 bonds, 154 residues, 1 model selected
+> select #7/B:27
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #7/B:27-34
+atoms, 62 bonds, 8 residues, 1 model selected
+> matchmaker #3/b:147-185 to #7/b:147-185
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_no_nuc.pdb, chain B (#7) with
+MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
+score = 186.6
+RMSD between 39 pruned atom pairs is 0.343 angstroms; (across all 39 pairs:
+.343)
+> select add #7
+atoms, 11571 bonds, 13 pseudobonds, 1452 residues, 3 models selected
+> select subtract #7
+Nothing selected
+> show #!3 models
+> surface hidePatches #3-4,7
+> color #3 darkgrey
+> hide #!3 models
+> show #!3 models
+> hide #!7 models
+> show #!7 models
+> hide #!3 models
+> hide #!7 models
+> show #!3 models
+> hide #!3 models
+> show #!7 models
+> select #7
+atoms, 11571 bonds, 13 pseudobonds, 1452 residues, 3 models selected
+> surface (#!7 & sel)
+> transparency (#!7 & sel) 60
+> select add #4
+atoms, 11571 bonds, 15 pseudobonds, 1452 residues, 9 models selected
+> select subtract #4
+atoms, 11571 bonds, 1 pseudobond, 1452 residues, 7 models selected
+> select subtract #7
+models selected
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> ui mousemode right zoom
+> label height 2.5
+[Repeated 1 time(s)]
+> ui mousemode right "move label"
+> ~distance #7/B:149@CA #7/C:149@CA
+> ~distance #7/B:151@CA #7/C:151@CA
+> ~distance #7/B:153@CA #7/C:153@CA
+> ~distance #7/B:155@CA #7/C:155@CA
+> ~distance #7/B:157@CA #7/C:157@CA
+> ~distance #7/B:159@CA #7/C:159@CA
+> ~distance #7/B:161@CA #7/C:161@CA
+> ~distance #7/B:163@CA #7/C:163@CA
+> ~distance #7/B:165@CA #7/C:165@CA
+> ~distance #7/B:169@CA #7/C:169@CA
+> ~distance #7/B:167@CA #7/C:167@CA
+> distance #7/B:169@ca #7/C:169@ca color black
+Distance between MolABC_no_nuc.pdb #7/B GLN 169 CA and /C GLN 169 CA: 15.265Å
+> label height 2.5
+[Repeated 1 time(s)]
+> ~distance #7/B:169@CA #7/C:169@CA
+> ~distance #7/B:171@CA #7/C:171@CA
+> hide #!7 models
+> open /Users/alexandrakaragiaridi/Desktop/MolABC_nuc_chains_renamed.pdb
+Chain information for MolABC_nuc_chains_renamed.pdb #8
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D E | No description available
+> ui mousemode right "translate selected models"
+> view
+> select #8
+atoms, 10549 bonds, 4 pseudobonds, 1316 residues, 2 models selected
+> hide sel atoms
+> show sel cartoons
+> select #8/A:23-341
+atoms, 1510 bonds, 3 pseudobonds, 187 residues, 2 models selected
+> color (#!8 & sel) yellow
+> select #8/B:7-331
+atoms, 2327 bonds, 1 pseudobond, 299 residues, 2 models selected
+> color (#!8 & sel) blue
+> select #8/C:6-331
+atoms, 2550 bonds, 326 residues, 1 model selected
+> color sel cornflower blue
+> select #8/D:2-252
+atoms, 2035 bonds, 251 residues, 1 model selected
+> color sel purple
+> select #8/E:2-252
+atoms, 2035 bonds, 251 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel violet
+> ~select
+Nothing selected
+> select #8/b,c
+atoms, 4877 bonds, 1 pseudobond, 625 residues, 2 models selected
+Alignment identifier is 8/B
+Alignment identifier is 8/C
+> ~select
+Nothing selected
+> select #8/B:146
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #8/B:7-146
+atoms, 876 bonds, 1 pseudobond, 114 residues, 2 models selected
+> cartoon hide (#!8 & sel)
+> select #8/B:172
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #8/B:172-331
+atoms, 1258 bonds, 160 residues, 1 model selected
+> cartoon hide sel
+> select #8/C:146
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #8/C:6-146
+atoms, 1099 bonds, 141 residues, 1 model selected
+> cartoon hide sel
+> select #8/C:172
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #8/C:172-331
+atoms, 1258 bonds, 160 residues, 1 model selected
+> cartoon hide sel
+> ~select
+Nothing selected
+> select #8/a,d,e
+atoms, 5580 bonds, 3 pseudobonds, 689 residues, 2 models selected
+> hide sel cartoons
+> select add #8
+atoms, 10549 bonds, 4 pseudobonds, 1316 residues, 2 models selected
+> select subtract #8
+Nothing selected
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> matchmaker #3/b:147-185 to #8/b:147-185
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_nuc_chains_renamed.pdb, chain B (#8) with
+MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
+score = 190.2
+RMSD between 39 pruned atom pairs is 0.552 angstroms; (across all 39 pairs:
+.552)
+> show #!3 models
+> hide #!3 models
+> distance #7/B:171@ca #7/C:171@ca color black
+Distance between MolABC_no_nuc.pdb #7/B ILE 171 CA and /C ILE 171 CA: 23.719Å
+> distance #8/B:171@ca #8/C:171@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B ILE 171 CA and /C ILE 171
+CA: 23.083Å
+> distance #8/B:169@ca #8/C:169@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B GLN 169 CA and /C GLN 169
+CA: 15.069Å
+> distance #8/B:167@ca #8/C:167@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B LEU 167 CA and /C LEU 167
+CA: 22.924Å
+> distance #8/B:165@ca #8/C:165@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B VAL 165 CA and /C VAL 165
+CA: 19.082Å
+> distance #8/B:163@ca #8/C:163@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B ALA 163 CA and /C ALA 163
+CA: 21.089Å
+> distance #8/B:161@ca #8/C:161@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B PHE 161 CA and /C PHE 161
+CA: 24.043Å
+> distance #8/B:159@ca #8/C:159@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B GLY 159 CA and /C GLY 159
+CA: 19.297Å
+> distance #8/B:157@ca #8/C:157@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B LEU 157 CA and /C LEU 157
+CA: 26.623Å
+> distance #8/B:155@ca #8/C:155@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B MET 155 CA and /C MET 155
+CA: 18.196Å
+> distance #8/B:153@ca #8/C:153@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B ILE 153 CA and /C ILE 153
+CA: 27.497Å
+> distance #8/B:151@ca #8/C:151@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B ILE 151 CA and /C ILE 151
+CA: 18.896Å
+> distance #8/B:149@ca #8/C:149@ca color black
+Distance between MolABC_nuc_chains_renamed.pdb #8/B MET 149 CA and /C MET 149
+CA: 26.821Å
+> label height 1.5
+[Repeated 1 time(s)]
+> ui mousemode right "move label"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> select #8
+atoms, 10549 bonds, 16 pseudobonds, 1316 residues, 3 models selected
+> show sel surfaces
+> transparency (#!8 & sel) 60
+> select subtract #8
+models selected
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> select ::name="ANP"
+atoms, 92 bonds, 2 residues, 1 model selected
+> show sel surfaces
+> color (#!8 & sel) forest green
+> ~select
+Nothing selected
+> label height 2.5
+[Repeated 1 time(s)]
+> ui mousemode right "move label"
+> ~distance #7/B:171@CA #7/C:171@CA
+> ~distance #8/B:149@CA #8/C:149@CA
+> ~distance #8/B:151@CA #8/C:151@CA
+> ~distance #8/B:153@CA #8/C:153@CA
+> ~distance #8/B:155@CA #8/C:155@CA
+> ~distance #8/B:157@CA #8/C:157@CA
+> ~distance #8/B:159@CA #8/C:159@CA
+> ~distance #8/B:161@CA #8/C:161@CA
+> ~distance #8/B:163@CA #8/C:163@CA
+> ~distance #8/B:165@CA #8/C:165@CA
+> ~distance #8/B:167@CA #8/C:167@CA
+> ~distance #8/B:169@CA #8/C:169@CA
+> ~distance #8/B:171@CA #8/C:171@CA
+> save /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs
+> hide #!4 models
+> hide #4.1 models
+> select #8
+atoms, 10549 bonds, 4 pseudobonds, 1316 residues, 7 models selected
+> cartoon (#!8 & sel)
+> select #8/a,d,e
+atoms, 5580 bonds, 3 pseudobonds, 689 residues, 2 models selected
+> cartoon hide (#!8 & sel)
+> surface hidePatches (#!8 & sel)
+> select ::name="ANP"
+atoms, 92 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> hide sel surfaces
+> select #8/d,e
+atoms, 4070 bonds, 502 residues, 1 model selected
+> show sel surfaces
+> ~select
+Nothing selected
+> hide #!8 models
+> show #!3 models
+> cartoon #3
+> ui mousemode right zoom
+> select #3/b
+atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
+> color (#!3 & sel) blue
+> select #3/c
+atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
+> color (#!3 & sel) cornflower blue
+> select #3/d
+atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
+> color (#!3 & sel) purple
+> select #3/e
+atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel violet
+> ~select
+Nothing selected
+> show #!5 models
+> color #5 darkgrey
+> matchmaker #3/b:147-185 to #5/b:147-185
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolBC_WT_in_C5_chains_renamed.pdb, chain B (#5) with
+MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
+score = 186.6
+RMSD between 39 pruned atom pairs is 0.534 angstroms; (across all 39 pairs:
+.534)
+> view
+> hide #!3,5 surfaces
+> cartoon #3,5
+> morph #3,5 frames 60
+Computed 61 frame morph #9
+> coordset #9 1,61
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
+> hide #!9 models
+> hide #4.1 models
+> show #!3 models
+> color #3 darkgrey
+> show #!7 models
+> view
+> hide #!3 models
+> view
+> hide #!7 surfaces
+> cartoon #7
+> matchmaker #3/b:147-185 to #7/b:147-185
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_no_nuc.pdb, chain B (#7) with
+MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
+score = 186.6
+RMSD between 39 pruned atom pairs is 0.343 angstroms; (across all 39 pairs:
+.343)
+> show #!3 models
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> morph #7,3 frames 60
+models have different number of chains, 5 (Morph - MolABC_no_nuc.pdb #/A,Morph
+- MolABC_no_nuc.pdb #/B,Morph - MolABC_no_nuc.pdb #/C,Morph -
+MolABC_no_nuc.pdb #/D,Morph - MolABC_no_nuc.pdb #/E) and 4
+(MolBC_WT_final_structure_chains_renamed.pdb
+#3/B,MolBC_WT_final_structure_chains_renamed.pdb
+#3/C,MolBC_WT_final_structure_chains_renamed.pdb
+#3/D,MolBC_WT_final_structure_chains_renamed.pdb #3/E)
+> open
+> /Users/alexandrakaragiaridi/Desktop/MolABC_no_nuc_everything/MolABC_no_nuc_MolA_deleted.pdb
+Chain information for MolABC_no_nuc_MolA_deleted.pdb #10
+---
+Chain | Description
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+> hide #!7 models
+> matchmaker #3/b:147-185 to #10/b:147-185
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
+MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
+score = 186.6
+RMSD between 39 pruned atom pairs is 0.343 angstroms; (across all 39 pairs:
+.343)
+> select #10/b
+atoms, 2496 bonds, 320 residues, 1 model selected
+> color sel blue
+> select #10/c
+atoms, 2465 bonds, 316 residues, 1 model selected
+> color sel cornflower blue
+> select #10/d
+atoms, 2043 bonds, 252 residues, 1 model selected
+> color sel purple
+> select #10/e
+atoms, 2035 bonds, 251 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel violet
+> ~select
+Nothing selected
+> select #3/b
+atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
+> ~select
+Nothing selected
+> morph #10,3 frames 60
+Computed 61 frame morph #11
+> coordset #11 1,61
+> ui mousemode right "translate selected models"
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
+> hide #!11 models
+> open /Users/alexandrakaragiaridi/Desktop/MolABC_nuc_MolA_deleted.pdb
+Chain information for MolABC_nuc_MolA_deleted.pdb #12
+---
+Chain | Description
+B | No description available
+C | No description available
+D E | No description available
+> view
+> select #12/b
+atoms, 2327 bonds, 1 pseudobond, 299 residues, 2 models selected
+> color (#!12 & sel) blue
+> select #12/c
+atoms, 2550 bonds, 326 residues, 1 model selected
+> color sel cornflower blue
+> select #12/d
+atoms, 2035 bonds, 251 residues, 1 model selected
+> color sel purple
+> select #12/e
+atoms, 2035 bonds, 251 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel violet
+> matchmaker #3/b:147-185 to #12/b:147-185
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_nuc_MolA_deleted.pdb, chain B (#12) with
+MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
+score = 190.2
+RMSD between 39 pruned atom pairs is 0.552 angstroms; (across all 39 pairs:
+.552)
+> show #!3 models
+> select add #12
+atoms, 9039 bonds, 1 pseudobond, 1129 residues, 2 models selected
+> select subtract #12
+Nothing selected
+> hide #!12 models
+> show #!8 models
+> surface hidePatches #3,8
+> cartoon #3,8
+> matchmaker #3/b:147-185 to #8/b:147-185
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_nuc_chains_renamed.pdb, chain B (#8) with
+MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
+score = 190.2
+RMSD between 39 pruned atom pairs is 0.552 angstroms; (across all 39 pairs:
+.552)
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> hide #!8 models
+> show #!12 models
+> ui mousemode right "translate selected models"
+> hide #!12 models
+> show #!8 models
+> hide #!8 models
+> show #!12 models
+> morph #12,3 frames 60
+Computed 61 frame morph #13
+> coordset #13 1,61
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
+> save /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs
+——— End of log from Fri Apr 4 15:35:46 2025 ———
+opened ChimeraX session
+> close #13
+> close #11
+> rename #3 MolBC_WT_final_structure_chains_renamed_cryo.pdb
+> show #!3 models
+> hide #!3 models
+> rename #1 MolBC_in_DM_chains_renamed.pdb
+> rename #3 MolBC_WT_in_DDM_chains_renamed_cryo.pdb
+> rename #8 MolABC_nuc.pdb
+> show #!8 models
+> hide #!8 models
+> show #!7 models
+> ui mousemode right "translate selected models"
+> select #7/b
+atoms, 2496 bonds, 320 residues, 1 model selected
+Alignment identifier is 7/B
+> ~select
+Nothing selected
+> show #!3 models
+> select #3/b
+atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
+Alignment identifier is 3/B
+> ~select
+Nothing selected
+> select #3/B:54-55
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #3/B:54-86
+atoms, 243 bonds, 33 residues, 1 model selected
+> select #7/B:52
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #7/B:52-87
+atoms, 270 bonds, 36 residues, 1 model selected
+> matchmaker #3/b:52-87 to #7/b:52-87
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_no_nuc.pdb, chain B (#7) with
+MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
+score = 176.5
+RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
+.157)
+> select add #7
+atoms, 11571 bonds, 1 pseudobond, 1452 residues, 3 models selected
+> select subtract #7
+models selected
+> color #3 #929292ff
+> color #3 #919191ff
+> color #3 #797979ff
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> hide #!7 models
+> show #10 models
+> matchmaker #3/b:52-87 to #10/b:52-87
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
+MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
+score = 176.5
+RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
+.157)
+> morph #3,10 frames 60
+Computed 61 frame morph #11
+> coordset #11 1,61
+> hide #!11 models
+> show #!3 models
+> show #10 models
+> morph #10,3 frames 60
+Computed 61 frame morph #13
+> coordset #13 1,61
+> morph #10,3 frames 100
+Computed 101 frame morph #14
+> coordset #14 1,101
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> close #13
+> close #14
+> show #!3 models
+> show #10 models
+> morph #3,10 frames 100
+Computed 101 frame morph #13
+> coordset #13 1,101
+> close #13
+> show #!3 models
+> show #10 models
+> morph #10,3 frames 60
+Computed 61 frame morph #13
+> coordset #13 1,61
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
+> hide #!13 models
+> show #!3 models
+> show #10 models
+> morph #3,10 frames 60
+Computed 61 frame morph #14
+> coordset #14 1,61
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Error processing trigger "new frame":
+Movie encoding failed because no images were recorded.
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
+> hide #!14 models
+> show #!3 models
+> show #!8 models
+> select #8/b
+atoms, 2327 bonds, 1 pseudobond, 299 residues, 2 models selected
+Alignment identifier is 8/B
+> ~select
+Nothing selected
+> matchmaker #3/b:56-87 to #8/b:56-87
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_nuc.pdb, chain B (#8) with
+MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
+score = 161.8
+RMSD between 32 pruned atom pairs is 0.522 angstroms; (across all 32 pairs:
+.522)
+> view
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> hide #!8 models
+> show #!12 models
+> matchmaker #3/b:56-87 to #8/b:56-87
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_nuc.pdb, chain B (#8) with
+MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
+score = 161.8
+RMSD between 32 pruned atom pairs is 0.522 angstroms; (across all 32 pairs:
+.522)
+> morph #12,3 frames 60
+Computed 61 frame morph #15
+> coordset #15 1,61
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
+> hide #!15 models
+> show #!3 models
+> show #!12 models
+> morph #3,12 frames 60
+Computed 61 frame morph #16
+> coordset #16 1,61
+> movie record
+> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
+Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
+> hide #!16 models
+> show #!3 models
+> show #10 models
+> matchmaker #3/b:52-87 to #10/b:52-87
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
+MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
+score = 176.5
+RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
+.157)
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> select #3/b
+atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
+> color (#!3 & sel) orange
+> color (#!3 & sel) orange red
+> select #3/c
+atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
+> color (#!3 & sel) forest green
+> ~select
+Nothing selected
+> select #3/c
+atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel saddle brown
+> select #3/d
+atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
+> ~select
+Nothing selected
+> select #3/d,e
+atoms, 3935 bonds, 5 pseudobonds, 486 residues, 3 models selected
+> cartoon hide (#!3 & sel)
+> select #10/d,e
+atoms, 4078 bonds, 503 residues, 1 model selected
+> cartoon hide sel
+> select add #10
+atoms, 9039 bonds, 1139 residues, 1 model selected
+> select subtract #10
+Nothing selected
+> ui mousemode right zoom
+> ui tool show "Side View"
+> ui tool show Axes/Planes/Centroids
+> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
+> ui tool show Axes/Planes/Centroids
+value: array([ 0, 0, 0, 255], dtype=uint8) default: None
+> define axis #3 perHelix true color black name "helix axes"
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 1'
+centered at [138.87288781 117.78180224 148.42755497] with direction [
+.0440841 -0.00343284 0.99902193], radius 1.84197, and length 21.5191
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 2'
+centered at [136.89511948 119.27405922 134.67479006] with direction [
+.08451804 -0.11156966 0.990156 ], radius 1.44753, and length 7.55249
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 3'
+centered at [144.01128977 114.05989748 123.60591038] with direction [0.9545536
+.24888157 0.16396765], radius 1.16133, and length 5.69625
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 4'
+centered at [146.98443498 118.23838681 127.30097697] with direction
+[0.67184113 0.719126 0.17744662], radius 1.92464, and length 5.88277
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 5'
+centered at [150.46413505 128.9089645 146.65778978] with direction [0.21556326
+.47619176 0.85251034], radius 1.85607, and length 39.0284
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 6'
+centered at [162.52256844 142.63940295 136.02828041] with direction [
+.27282382 0.02254532 -0.96179981], radius 1.84926, and length 23.1877
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 7'
+centered at [168.38900361 139.87104636 144.90354783] with direction
+[0.21440203 0.43472652 0.87466829], radius 1.95697, and length 38.1453
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 8'
+centered at [161.37459523 151.28871478 143.12819413] with direction
+[-0.02791598 0.14852199 -0.98851501], radius 1.84012, and length 35.7778
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 9'
+centered at [154.88027968 145.06608012 126.7136637 ] with direction
+[-0.53965869 -0.36466803 0.75880546], radius 1.73624, and length 11.5571
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 10'
+centered at [152.01490142 141.38744199 133.65031613] with direction
+[-0.73611941 -0.00082326 0.67685119], radius 1.13652, and length 5.92586
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 11'
+centered at [159.02791703 123.43494192 138.60155144] with direction
+[0.21299364 0.08258235 0.97355732], radius 1.85904, and length 16.6781
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 12'
+centered at [158.72486474 123.11321475 157.3782829 ] with direction
+[-0.3437473 0.03748733 0.93831364], radius 1.80163, and length 7.70168
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 13'
+centered at [156.82043946 130.61392236 167.52160805] with direction
+[-0.13681146 -0.9079335 -0.39615575], radius 1.76316, and length 8.14729
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 14'
+centered at [161.73668965 138.4798262 174.91852687] with direction [
+.08864439 0.92407725 -0.3717841 ], radius 1.56342, and length 5.87844
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 15'
+centered at [163.97384547 134.12606164 177.32571777] with direction [
+.28048337 0.89218889 -0.35401705], radius 1.19567, and length 5.28539
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 16'
+centered at [161.6792009 133.69839711 150.6143826 ] with direction
+[-0.35567372 -0.03245447 -0.93404652], radius 1.90371, and length 32.7461
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 17'
+centered at [142.47807596 133.57148003 155.82946554] with direction
+[-0.76939881 -0.0574665 0.63617849], radius 1.58457, and length 5.65891
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 18'
+centered at [140.21990568 130.59778964 159.96782242] with direction
+[-0.66910528 0.00110959 0.7431668 ], radius 1.16549, and length 5.71771
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 19'
+centered at [143.31329819 127.50429047 147.60887881] with direction
+[-0.34152171 0.19224759 -0.92000206], radius 1.94095, and length 36.4169
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 20'
+centered at [139.04079142 140.67324534 145.03288008] with direction
+[-0.45861454 0.15994128 0.87412327], radius 1.91368, and length 23.535
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 1'
+centered at [163.2294379 183.2483208 147.72816911] with direction [ 0.16232497
+-0.06729814 -0.98443972], radius 1.84785, and length 19.9747
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 2'
+centered at [166.38264193 181.34888562 135.02965093] with direction [
+.18614011 -0.1161945 -0.97562836], radius 1.46901, and length 7.42552
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 3'
+centered at [151.14751531 171.39665553 147.30930401] with direction
+[-0.28843731 -0.47151966 0.83335054], radius 1.88144, and length 38.8998
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 4'
+centered at [140.48527463 158.01748359 134.72758194] with direction
+[-0.19079639 -0.05488875 -0.98009385], radius 1.84209, and length 23.4331
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 5'
+centered at [134.27304968 161.20652608 142.78627861] with direction
+[-0.24658266 -0.42045288 0.87316457], radius 1.88261, and length 33.9177
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 6'
+centered at [140.98274908 150.00170498 143.83752847] with direction [
+.09536412 -0.19142402 -0.97686362], radius 1.85161, and length 39.0487
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 7'
+centered at [148.55019275 154.95279448 125.67151223] with direction
+[0.33479868 0.28666457 0.89762646], radius 1.71026, and length 10.2146
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 8'
+centered at [150.6232085 158.76590252 131.58822087] with direction
+[-0.26684054 0.15585634 0.95105464], radius 1.16158, and length 5.76255
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 9'
+centered at [143.13144099 177.5436752 142.77452959] with direction
+[-0.16046819 0.01701625 0.98689432], radius 1.9463, and length 26.8796
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 10'
+centered at [143.02837214 178.22286017 158.7754407 ] with direction
+[-0.38096048 -0.31575783 0.86900294], radius 1.20412, and length 5.28596
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 11'
+centered at [143.59843255 170.15589851 166.53285951] with direction [
+.04918429 -0.95745313 0.28436667], radius 1.5971, and length 11.0317
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 12'
+centered at [137.99810081 163.55370792 173.5505006 ] with direction
+[-0.06121785 -0.94362406 -0.32530908], radius 1.57972, and length 5.69983
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 13'
+centered at [135.58382444 167.90992901 175.61219975] with direction
+[-0.25305438 -0.90434208 -0.34369883], radius 1.19961, and length 5.28161
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 14'
+centered at [140.04917237 167.45543663 149.47364086] with direction [
+.41500885 0.01046323 -0.90975721], radius 1.89122, and length 32.139
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 15'
+centered at [159.99254977 169.7174672 158.21270651] with direction [0.45613914
+.56166159 0.69027048], radius 1.79128, and length 12.5526
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 16'
+centered at [152.43981866 175.99254125 160.74627567] with direction
+[-0.29572772 0.05698523 0.95357108], radius 1.81357, and length 7.71215
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 17'
+centered at [160.47513667 173.0101247 144.08830691] with direction [
+.43750857 -0.28211725 -0.85381269], radius 1.85399, and length 31.2751
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 18'
+centered at [163.57342427 160.32346648 147.29998901] with direction [
+.31244959 -0.09350065 0.94532158], radius 2.0372, and length 26.3918
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 1'
+centered at [167.87615649 143.04389693 185.98121469] with direction [ 0.438123
+-0.83562973 -0.33131737], radius 1.81012, and length 14.1925
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 2'
+centered at [147.6201987 127.68936813 176.62184077] with direction [
+.93725005 0.16662752 -0.30626395], radius 1.56131, and length 6.06092
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 3'
+centered at [154.95568202 126.20793828 177.58107552] with direction [
+.95898997 -0.26644434 -0.09667287], radius 1.44573, and length 10.0638
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 4'
+centered at [151.15600715 118.6019877 181.57814446] with direction
+[-0.37732147 0.56479719 0.73391596], radius 1.79916, and length 17.2473
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 5'
+centered at [146.55331579 123.39381244 190.23537683] with direction [
+.04673215 -0.81899731 -0.57189118], radius 1.1843, and length 5.42106
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 6'
+centered at [140.73208295 135.93343584 177.58493265] with direction
+[-0.81812109 0.45557423 0.35089885], radius 1.15152, and length 5.77568
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 7'
+centered at [148.98351106 133.34372209 185.7268084 ] with direction [
+.77026349 -0.62284617 -0.13695546], radius 1.81761, and length 18.4936
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 8'
+centered at [157.23115414 125.30149438 184.62927987] with direction [
+.67554073 -0.41725825 -0.60789825], radius 1.1514, and length 5.8277
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 9'
+centered at [150.063202 134.06961112 197.9082053 ] with direction [ 0.72695201
+-0.66523867 0.17028885], radius 1.85312, and length 24.2887
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 10'
+centered at [155.63590787 142.9646218 203.72317399] with direction
+[-0.12131521 0.97595014 -0.1811186 ], radius 1.6972, and length 11.4219
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 11'
+centered at [165.59051581 144.79740981 209.25865921] with direction [
+.40157598e-01 8.97920524e-01 -1.47057412e-04], radius 1.57329, and length
+.79026
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 12'
+centered at [163.52091577 156.28680447 205.36494461] with direction [
+.06439306 -0.36066782 0.93046884], radius 1.86281, and length 11.8846
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 1'
+centered at [130.87501269 159.11892998 184.2442496 ] with direction
+[-0.40949696 0.82601253 -0.3873184 ], radius 1.80496, and length 14.0558
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 2'
+centered at [151.85163649 174.25343037 176.03807778] with direction
+[-0.92231263 -0.17427807 -0.34491532], radius 1.56122, and length 5.9922
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 3'
+centered at [144.50157861 175.78058157 176.35465875] with direction
+[-0.94732324 0.25522088 -0.19349673], radius 1.44096, and length 10.1801
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 4'
+centered at [148.57410773 182.91758455 181.91135025] with direction [
+.33102847 -0.46584117 0.82061694], radius 1.85479, and length 20.4498
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 5'
+centered at [159.11810243 177.16289377 183.66867963] with direction [
+.28986355 -0.6503084 -0.70219521], radius 1.14027, and length 5.99708
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 6'
+centered at [149.76839231 168.9091345 185.16992042] with direction
+[-0.75513013 0.61647857 -0.22300821], radius 1.81515, and length 18.5125
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 7'
+centered at [141.64126568 176.89330933 183.09126614] with direction
+[-0.62885264 0.41150727 -0.65970155], radius 1.14434, and length 5.9151
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 8'
+centered at [147.24134326 169.09583718 197.32862548] with direction
+[-0.71026615 0.69813961 0.09012817], radius 1.90461, and length 25.5463
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 9'
+centered at [141.63445911 159.08325547 202.95746234] with direction
+[-0.06815874 0.94742795 0.31262545], radius 1.63707, and length 10.4006
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 10'
+centered at [131.09207528 158.14926242 207.79433463] with direction
+[-0.49510089 -0.86657585 -0.06262105], radius 1.57904, and length 5.37778
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 11'
+centered at [133.55097158 146.50628731 204.2284949 ] with direction
+[-0.15420662 0.41363509 0.89728832], radius 1.8638, and length 11.9168
+chain B helix 1 #3.6.1 to chain B helix 2 #3.6.2: distance: 1.279Å; angle:
+.6°
+> select down
+Nothing selected
+> select down
+Nothing selected
+> select down
+Nothing selected
+> select down
+Nothing selected
+> select down
+Nothing selected
+> close #3.6.1-61
+> ui tool show Axes/Planes/Centroids
+value: array([ 0, 0, 0, 255], dtype=uint8) default: None
+> define axis #3 perHelix true color black name "helix axes" radius 0.2
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 1'
+centered at [138.87288781 117.78180224 148.42755497] with direction [
+.0440841 -0.00343284 0.99902193], radius 0.2, and length 21.5191
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 2'
+centered at [136.89511948 119.27405922 134.67479006] with direction [
+.08451804 -0.11156966 0.990156 ], radius 0.2, and length 7.55249
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 3'
+centered at [144.01128977 114.05989748 123.60591038] with direction [0.9545536
+.24888157 0.16396765], radius 0.2, and length 5.69625
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 4'
+centered at [146.98443498 118.23838681 127.30097697] with direction
+[0.67184113 0.719126 0.17744662], radius 0.2, and length 5.88277
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 5'
+centered at [150.46413505 128.9089645 146.65778978] with direction [0.21556326
+.47619176 0.85251034], radius 0.2, and length 39.0284
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 6'
+centered at [162.52256844 142.63940295 136.02828041] with direction [
+.27282382 0.02254532 -0.96179981], radius 0.2, and length 23.1877
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 7'
+centered at [168.38900361 139.87104636 144.90354783] with direction
+[0.21440203 0.43472652 0.87466829], radius 0.2, and length 38.1453
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 8'
+centered at [161.37459523 151.28871478 143.12819413] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 9'
+centered at [154.88027968 145.06608012 126.7136637 ] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 10'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 11'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 12'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 13'
+centered at [156.82043946 130.61392236 167.52160805] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 14'
+centered at [161.73668965 138.4798262 174.91852687] with direction [
+.08864439 0.92407725 -0.3717841 ], radius 0.2, and length 5.87844
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 15'
+centered at [163.97384547 134.12606164 177.32571777] with direction [
+.28048337 0.89218889 -0.35401705], radius 0.2, and length 5.28539
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 16'
+centered at [161.6792009 133.69839711 150.6143826 ] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 17'
+centered at [142.47807596 133.57148003 155.82946554] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 18'
+centered at [140.21990568 130.59778964 159.96782242] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 19'
+centered at [143.31329819 127.50429047 147.60887881] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 20'
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+-0.06729814 -0.98443972], radius 0.2, and length 19.9747
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 2'
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+.18614011 -0.1161945 -0.97562836], radius 0.2, and length 7.42552
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 3'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 4'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 5'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 6'
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+.09536412 -0.19142402 -0.97686362], radius 0.2, and length 39.0487
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 7'
+centered at [148.55019275 154.95279448 125.67151223] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 8'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 9'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 10'
+centered at [143.02837214 178.22286017 158.7754407 ] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 11'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 12'
+centered at [137.99810081 163.55370792 173.5505006 ] with direction
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 13'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 14'
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+.56166159 0.69027048], radius 0.2, and length 12.5526
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 16'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 17'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 18'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 2'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 3'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 4'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 6'
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+-0.66523867 0.17028885], radius 0.2, and length 24.2887
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 10'
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+.40157598e-01 8.97920524e-01 -1.47057412e-04], radius 0.2, and length 5.79026
+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 12'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 2'
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+Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 5'
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+value: array([255, 212, 121, 255], dtype=uint8) default: None
+> define axis #10 perHelix true color #ffd479 name "helix axes" radius 0.2
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+-0.02481161 -0.99914014], radius 0.2, and length 21.8343
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 2' centered
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+.08491942 -0.99631003], radius 0.2, and length 7.63264
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 3' centered
+at [138.05372817 108.06764281 128.51475989] with direction [ 0.8026101
+-0.59184527 0.07440569], radius 0.2, and length 18.5767
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 4' centered
+at [145.72161104 116.33145977 124.84189419] with direction [0.1508822
+.53938742 0.8284297 ], radius 0.2, and length 16.9619
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 5' centered
+at [150.81669695 129.65128059 147.93503227] with direction [0.22863824
+.50193185 0.83413966], radius 0.2, and length 38.3494
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 6' centered
+at [155.28565702 143.07274943 150.93031609] with direction [0.52188408
+.82517202 0.21616696], radius 0.2, and length 6.46639
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 7' centered
+at [161.4682541 142.4935721 136.67182626] with direction [ 0.20901679
+-0.00098958 -0.97791155], radius 0.2, and length 21.903
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 8' centered
+at [167.8756954 139.366525 144.05325253] with direction [0.21956307 0.43124242
+.87511258], radius 0.2, and length 36.8449
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 9' centered
+at [160.91926351 150.94322402 144.77402766] with direction [-0.05428096
+.15150463 -0.98696501], radius 0.2, and length 38.4235
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 10' centered
+at [153.16255893 144.72955059 127.98594293] with direction [-0.39611073
+-0.47095447 0.7882247 ], radius 0.2, and length 12.3565
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 11' centered
+at [159.05351081 123.17544409 145.89835395] with direction [0.04832853
+.00678212 0.99880847], radius 0.2, and length 30.5075
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 12' centered
+at [156.62467727 129.23983617 166.64295286] with direction [-0.60476875
+.72433613 0.33104672], radius 0.2, and length 5.7345
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 13' centered
+at [157.41472133 133.74646525 168.35308858] with direction [ 0.28281302
+-0.91915742 0.27416498], radius 0.2, and length 5.7588
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 14' centered
+at [163.09860358 136.86333389 175.22680129] with direction [ 0.34520149
+-0.79444064 0.49969992], radius 0.2, and length 10.8468
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 15' centered
+at [161.69075667 133.55055861 150.55871106] with direction [-0.36743289
+-0.02621678 -0.92968046], radius 0.2, and length 32.6292
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 16' centered
+at [141.58698056 132.34284382 157.58710316] with direction [-0.29675497
+-0.608367 0.73608836], radius 0.2, and length 15.2808
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 17' centered
+at [143.12102326 127.70175984 146.94348142] with direction [-0.3506446
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+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 18' centered
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+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 1' centered
+at [163.29064596 182.64512887 148.75598259] with direction [-0.05834301
+.00278421 0.99829271], radius 0.2, and length 21.7356
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 2' centered
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+.07495203 0.99532432], radius 0.2, and length 7.38453
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 3' centered
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+.5813858 0.04389144], radius 0.2, and length 18.5121
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 4' centered
+at [157.45680002 184.37817105 123.8528681 ] with direction [-0.32193823
+-0.50009725 0.80390206], radius 0.2, and length 14.3044
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 5' centered
+at [151.36637968 172.18926675 146.45943825] with direction [-0.2624205
+-0.46650916 0.84469206], radius 0.2, and length 38.9625
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 6' centered
+at [139.79168852 158.62661407 136.63319875] with direction [-0.20785876
+-0.01337435 -0.97806741], radius 0.2, and length 21.8971
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 7' centered
+at [133.6554324 161.4499327 144.85609143] with direction [-0.24901695
+-0.43824913 0.86367139], radius 0.2, and length 28.8519
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 8' centered
+at [140.13677409 149.89764288 143.42844734] with direction [ 0.05595601
+-0.15755276 -0.98592396], radius 0.2, and length 35.6621
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 9' centered
+at [148.28963686 155.95675428 127.59072569] with direction [0.45002321
+.52608488 0.72160503], radius 0.2, and length 9.98349
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 10' centered
+at [150.0577348 159.38419006 133.64248285] with direction [ 0.65314182
+-0.01925877 0.75699066], radius 0.2, and length 5.7923
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 11' centered
+at [142.89437046 178.30495372 145.65238848] with direction [-0.06655957
+-0.00993754 0.99773296], radius 0.2, and length 30.3111
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 12' centered
+at [144.66131052 173.82859124 165.72848631] with direction [-0.12653854
+-0.9912196 -0.03836286], radius 0.2, and length 5.90297
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 13' centered
+at [143.98287464 167.83074192 168.24932632] with direction [-0.27621718
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+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 14' centered
+at [138.04156465 165.70742773 175.38542078] with direction [-0.22092881
+.89691282 0.38306377], radius 0.2, and length 11.423
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 15' centered
+at [139.6405478 167.88023035 151.11277642] with direction [ 0.3546893
+.01839823 -0.93480319], radius 0.2, and length 34.6455
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 16' centered
+at [160.210276 168.69872157 158.12497637] with direction [0.49255082
+.48463911 0.7228545 ], radius 0.2, and length 12.405
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 17' centered
+at [158.65506626 173.21794452 146.9061338 ] with direction [ 0.34973132
+-0.20483791 -0.91418239], radius 0.2, and length 37.8498
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 18' centered
+at [161.04181351 161.02595429 140.82768715] with direction [ 0.62687875
+-0.11819244 0.77009972], radius 0.2, and length 14.1207
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 1' centered
+at [168.76700144 141.7958998 185.53240035] with direction [ 0.41814452
+-0.85006236 -0.32023295], radius 0.2, and length 14.3046
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 2' centered
+at [148.24594739 127.49258116 176.58352434] with direction [ 0.94351814
+.14475109 -0.29802793], radius 0.2, and length 5.90175
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 3' centered
+at [155.45300825 125.8189693 177.34230037] with direction [ 0.94930299
+-0.28394858 -0.13489639], radius 0.2, and length 10.0409
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 4' centered
+at [151.10493761 119.20162945 182.35952123] with direction [-0.37011828
+.49951086 0.78326328], radius 0.2, and length 14.4107
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 5' centered
+at [147.40439667 123.05661258 190.19266188] with direction [-0.00875559
+-0.79589813 -0.60536725], radius 0.2, and length 5.44482
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 6' centered
+at [141.57140032 136.12936891 177.8823915 ] with direction [-0.77937561
+.4911306 0.38905578], radius 0.2, and length 5.93556
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 7' centered
+at [149.95074934 133.06815503 185.7198464 ] with direction [ 0.74252233
+-0.64996276 -0.16189194], radius 0.2, and length 18.616
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 8' centered
+at [157.89141083 124.64099433 184.3669659 ] with direction [ 0.63240665
+-0.47596771 -0.61116002], radius 0.2, and length 6.00605
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 9' centered
+at [151.32947596 133.32780545 197.91343184] with direction [ 0.71144945
+-0.68998224 0.13328237], radius 0.2, and length 24.2622
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 10' centered
+at [157.32927478 142.29031805 203.75612885] with direction [ 0.08528956
+-0.98386135 0.15729762], radius 0.2, and length 11.4332
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 11' centered
+at [167.45280133 143.21626877 209.07861051] with direction [ 0.51964799
+.85435156 -0.00702718], radius 0.2, and length 5.78006
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 12' centered
+at [165.55567951 155.12922861 205.26760417] with direction [ 0.14497464
+-0.39113787 0.90884186], radius 0.2, and length 12.0269
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 1' centered
+at [133.39473484 157.07146631 185.87999495] with direction [-0.39860215
+.88157301 -0.2528742 ], radius 0.2, and length 19.4134
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 2' centered
+at [153.07830876 173.80337272 176.46874051] with direction [-0.94017596
+-0.14546857 -0.30807153], radius 0.2, and length 6.02798
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 3' centered
+at [146.70080408 175.02852424 177.22092458] with direction [-9.91926295e-01
+.33135128e-04 -1.26815273e-01], radius 0.2, and length 7.52775
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 4' centered
+at [150.481171 182.85501584 182.3381486 ] with direction [ 0.32582667
+-0.48308072 0.81269306], radius 0.2, and length 20.9936
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 5' centered
+at [160.68109744 176.30491972 183.96304867] with direction [ 0.24314391
+-0.60924617 -0.75478484], radius 0.2, and length 6.12268
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 6' centered
+at [159.7829355 165.1504365 177.91728631] with direction [ 0.80732077
+-0.4232423 0.41121665], radius 0.2, and length 5.72695
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 7' centered
+at [151.26069892 168.44683323 185.62348711] with direction [-0.73463437
+.65423124 -0.17970486], radius 0.2, and length 18.5879
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 8' centered
+at [143.49635171 176.86572021 184.07650532] with direction [-0.61488979
+.45748837 -0.6423511 ], radius 0.2, and length 5.84625
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 9' centered
+at [149.7592522 168.1814334 197.81316584] with direction [-0.71101184
+.69313967 0.11840424], radius 0.2, and length 24.3445
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 10' centered
+at [143.7666456 159.45212789 203.61703639] with direction [ 0.08102842
+-0.98798961 -0.13157097], radius 0.2, and length 11.5155
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 11' centered
+at [133.80269407 159.30297004 209.29743794] with direction [-0.52713162
+-0.58705225 0.61441184], radius 0.2, and length 5.77119
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 12' centered
+at [135.3884304 146.52843308 205.04864675] with direction [-0.12217055
+.41913337 0.89966748], radius 0.2, and length 11.9003
+chain D helix 1 #3.7.39 to chain D helix 2 #3.7.40: distance: 15.139Å; angle:
+.1°
+> close #3.7.39-61
+chain E helix 10 to chain E helix 11: distance: 6.298Å; angle: 70.2°
+chain E helix 11 #10.1.59 to chain E helix 12 #10.1.60: distance: 7.725Å;
+angle: 68.2°
+> close #10.1.37-60
+chain E helix 11 to chain E helix 12: distance: 7.725Å; angle: 68.2°
+> ui mousemode right "translate selected models"
+> select #3.7.1
+model selected
+> select #10/d,e
+atoms, 4078 bonds, 503 residues, 1 model selected
+> cartoon sel
+> select #3/d,e
+atoms, 3935 bonds, 5 pseudobonds, 486 residues, 3 models selected
+> cartoon (#!3 & sel)
+> view matrix models
+> #3,0.96671,0.25077,0.050765,-11.242,0.25302,-0.96646,-0.043981,247.19,0.038033,0.055362,-0.99774,263.7,#4,1,0,0,0,0,1,0,0,0,0,1,0
+> matchmaker #3/b:52-87 to #10/b:52-87
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
+MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
+score = 176.5
+RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
+.157)
+> select #3.7.1
+model selected
+> ~select #3.7.1
+Nothing selected
+> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
+> select #10/d,e
+atoms, 4078 bonds, 503 residues, 1 model selected
+> cartoon hide sel
+> select #3/d,e
+atoms, 3935 bonds, 5 pseudobonds, 486 residues, 3 models selected
+> cartoon hide (#!3 & sel)
+> select add #4
+atoms, 3935 bonds, 6 pseudobonds, 486 residues, 6 models selected
+> select subtract #4
+atoms, 3935 bonds, 4 pseudobonds, 486 residues, 4 models selected
+> view matrix models
+> #3,0.96671,0.25077,0.050765,-15.154,0.25302,-0.96646,-0.043981,247.55,0.038033,0.055362,-0.99774,284.39
+> select add #3
+atoms, 8591 bonds, 9 pseudobonds, 1084 residues, 45 models selected
+> select subtract #3
+models selected
+> matchmaker #3/b:52-87 to #10/b:52-87
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
+MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
+score = 176.5
+RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
+.157)
+> select #3/b
+atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
+Alignment identifier is 3/B
+> select #10/b
+atoms, 2496 bonds, 320 residues, 1 model selected
+Alignment identifier is 10/B
+> ~select
+Nothing selected
+> select #3/B:9
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/B:9-26
+atoms, 130 bonds, 18 residues, 1 model selected
+> ~select
+Nothing selected
+> ui tool show "Color Actions"
+> ui mousemode right zoom
+> cartoon style #3,10 modeHelix tube sides 20
+> ui tool show Angles/Torsions
+Either three or four atoms must be selected!
+> cartoon style #3,10 modeHelix tube sides 20
+> cartoon style #3,10 xsection oval modeHelix default
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> hide #!10 models
+> hide #!3 models
+> open
+> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_DDM_chains_renamed.pdb
+Chain information for MolBC_WT_in_DDM_chains_renamed.pdb #17
+---
+Chain | Description
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+> rename #17 MolBC_WT_in_DDM_chains_renamed_test.pdb
+> open
+> /Users/alexandrakaragiaridi/Desktop/MolABC_no_nuc_everything/MolABC_no_nuc_MolA_deleted.pdb
+Chain information for MolABC_no_nuc_MolA_deleted.pdb #18
+---
+Chain | Description
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+> rename #18 MolABC_no_nuc_MolA_deleted_test.pdb
+> matchmaker #17/b:52-87 to #18/b:52-87
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MolABC_no_nuc_MolA_deleted_test.pdb, chain B (#18) with
+MolBC_WT_in_DDM_chains_renamed_test.pdb, chain B (#17), sequence alignment
+score = 176.5
+RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
+.157)
+> view
+> select #18/b
+atoms, 2496 bonds, 320 residues, 1 model selected
+> color sel blue
+> select #18/c
+atoms, 2465 bonds, 316 residues, 1 model selected
+> color sel cornflower blue
+> select #17/c
+atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel saddle brown
+> select #17/b
+atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
+> color (#!17 & sel) orange red
+> ~select
+Nothing selected
+> measure rotation #17 toModel #18 showSlabs true
+Position of MolBC_WT_in_DDM_chains_renamed_test.pdb #17 relative to
+MolABC_no_nuc_MolA_deleted_test.pdb #18 coordinates:
+Matrix rotation and translation
+.96671388 0.25077316 0.05076500 -13.12646901
+.25301729 -0.96646153 -0.04398133 247.98830480
+.03803308 0.05536179 -0.99774173 274.25174590
+Axis 0.99163829 0.12708940 0.02240077
+Axis point 0.00000000 121.37679976 140.36816995
+Rotation angle (degrees) 177.12883000
+Shift along axis 24.64342675
+> hide #!20 models
+> hide #20.1 models
+> hide #20.2 models
+> hide #19 models
+> hide #!17 models
+> hide #18 models
+> show #!12 models
+> show #!3 models
+> hide #!12 models
+> show #!10 models
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> select #3/c:194
+atoms, 15 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #10/c:194
+atoms, 15 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select add #10
+atoms, 9039 bonds, 1139 residues, 38 models selected
+> select subtract #10
+Nothing selected
+> ui mousemode right "translate selected models"
+Either three or four atoms must be selected!
+> select #10/c:194
+atoms, 15 bonds, 1 residue, 1 model selected
+> ui mousemode right select
+Drag select of 20 atoms, 23 bonds, 1 residues
+Either three or four atoms must be selected!
+> select #10/c:194
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #3/c:194
+atoms, 15 bonds, 1 residue, 1 model selected
+Either three or four atoms must be selected!
+> ~select
+Nothing selected
+No atoms selected
+> angle
+Missing or invalid "objects" argument: empty atom specifier
+> select #3.7.29
+model selected
+> select #10.1.29
+model selected
+> angle 3.7.29 to 10.1.29
+Missing or invalid "objects" argument: invalid objects specifier
+> angle 3.7.29, 10.1.29
+Missing or invalid "objects" argument: invalid objects specifier
+> angle 3.7.29 10.1.29
+Missing or invalid "objects" argument: invalid objects specifier
+> angle @3.7.29 @10.1.29
+Missing or invalid "objects" argument: only initial part "@3" of atom
+specifier valid
+> angle @3.7.29, @10.1.29
+Missing or invalid "objects" argument: only initial part "@3" of atom
+specifier valid
+> angle @3.7.29 to @10.1.29
+Missing or invalid "objects" argument: only initial part "@3" of atom
+specifier valid
+Either three or four atoms must be selected!
+> angle #3.7.29@ca to #10.1.29@ca
+Expected a number or a keyword
+> select #3.7.29
+model selected
+chain C helix 9 #3.7.29 to chain C helix 11 #10.1.29: distance: 245.802Å;
+angle: 5.6°
+> select add #3
+atoms, 8591 bonds, 9 pseudobonds, 1084 residues, 43 models selected
+> select subtract #3
+models selected
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> hide #!3,10 atoms
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> view orient
+> view
+> ui tool show "Side View"
+> view
+> ui mousemode right zoom
+> cartoon style #3,10 modeHelix tube sides 20
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> hide #!3 models
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> show #!3 models
+> hide #!3 models
+> select #10.1.1
+model selected
+> ~select #10.1.1
+Nothing selected
+> cartoon style #10.1.1#!10#!10.1 xsection oval modeHelix default
+> select #10.1.1
+model selected
+> ~select #10.1.1
+Nothing selected
+> show #!3 models
+> cartoon style #3#10.1.2-5#!10#!10.1 xsection oval modeHelix default
+> hide #!3 models
+> cartoon style #10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 modeHelix tube sides
+> 20
+> cartoon style #10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 xsection oval
+> modeHelix default
+> cartoon style #10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 modeHelix tube sides
+> 20
+> show #!3 models
+> cartoon style #3#10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 modeHelix tube sides
+> 20
+> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
+> cartoon style #3#10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 xsection oval
+> modeHelix default
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+chain B helix 2 #3.7.2 to chain B helix 2 #10.1.2: distance: 270.676Å; angle:
+.4°
+chain B helix 1 #3.7.1 to chain B helix 1 #10.1.1: distance: 242.099Å; angle:
+.7°
+> ui mousemode right "translate selected models"
+> preset cartoons/nucleotides licorice/ovals
+Using preset: Cartoons/Nucleotides / Licorice/Ovals
+Changed 21584 atom styles
+Preset expands to these ChimeraX commands:
+    show nucleic
+    hide protein|solvent|H
+    surf hide
+    style (protein|nucleic|solvent) & @@draw_mode=0 stick
+    cartoon
+    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
+    cartoon style ~(nucleic|strand) x round
+    cartoon style (nucleic|strand) x rect
+    cartoon style protein modeh default arrows f x round width 1 thick 1
+    cartoon style nucleic x round width 1.6 thick 1.6
+    nucleotides tube/slab shape ellipsoid
+> select #3/d,e
+atoms, 3935 bonds, 5 pseudobonds, 486 residues, 3 models selected
+> cartoon hide (#!3 & sel)
+> select #10/d,e
+atoms, 4078 bonds, 503 residues, 1 model selected
+> cartoon hide sel
+> cartoon style protein modeHelix default arrows false xsection round width
+> 0.2 thickness 0.3
+> select add #10
+atoms, 9039 bonds, 1139 residues, 38 models selected
+> select subtract #10
+Nothing selected
+> cartoon style #3,10 modeHelix tube sides 20
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!11 models
+> hide #!11 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> cartoon style #3,10 xsection oval modeHelix default
+> cartoon style #3,10 modeHelix tube sides 20
+> hide #!10 models
+> cartoon style #3 xsection oval modeHelix default
+> cartoon style #3 modeHelix tube sides 20
+> show #!10 models
+> cartoon style #3,10 xsection rectangle modeHelix default
+> cartoon style (#3,10 & coil) xsection oval
+> cartoon style #3,10 xsection barbell modeHelix default
+> cartoon style #3,10 modeHelix tube sides 20
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> hide #!10 models
+> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
+> show #!10 models
+> hide #!3 models
+> save /Users/alexandrakaragiaridi/Desktop/image5.png supersample 3
+> show #!3 models
+> save /Users/alexandrakaragiaridi/Desktop/image6.png supersample 3
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> hide #!3 models
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> show #!3 models
+> hide #!10 models
+> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
+> show #!10 models
+> transparency #3 0.5
+> transparency #3 0.5 target c
+> transparency #3 0.7 target c
+> transparency #3 0 target c
+> transparency #10 0.5 target c
+> transparency #10 0.5 target r
+> transparency #10 50 target r
+> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
+> transparency #10 70 target r
+> save /Users/alexandrakaragiaridi/Desktop/image5.png supersample 3
+> hide #!3 models
+> show #!3 models
+> transparency #3 50 target r
+> save /Users/alexandrakaragiaridi/Desktop/image6.png supersample 3
+> transparency #3 0 target r
+> transparency #3=10 0 target r
+Missing or invalid "percent" argument: Expected a number
+> transparency #10 0 target r
+> hide #!3 models
+> show #!3 models
+> ui mousemode right zoom
+> hide #!3 models
+> show #!3 models
+> transparency #10 0.5 target r
+> transparency #10 0 target r
+> transparency #10 0.6 target r
+> transparency #10 0.7 target r
+> transparency #10 70 target r
+> transparency #10 50 target r
+> transparency #10 0 target r
+> transparency #10 70 target r
+> transparency #10 0 target r
+> cartoon style #3,10 xsection oval modeHelix default
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+chain B helix 1 #10.1.1 to chain B helix 1 #3.7.1: distance: 242.099Å; angle:
+.7°
+chain B helix 2 #10.1.2 to chain B helix 2 #3.7.2: distance: 270.676Å; angle:
+.4°
+> select #3.7.5
+model selected
+> ~select #3.7.5
+Nothing selected
+> select #10.1.5
+model selected
+> ~select #10.1.5
+Nothing selected
+chain B helix 5 #3.7.5 to chain B helix 5 #10.1.5: distance: 119.069Å; angle:
+.0°
+> select #3.7.3
+model selected
+> select #10.1.4
+model selected
+> select #3.7.3
+model selected
+chain B helix 3 #3.7.3 to chain B helix 4 #10.1.4: distance: 87.665Å; angle:
+.5°
+No visible atoms or bonds selected
+> ~select #3.7.3
+Nothing selected
+> cartoon style #3.1-6#3.7.1-5#10.1.1-5#!3,10#!3.7#!10.1 modeHelix tube sides
+> 20
+> cartoon style #3.1-6#3.7.1-5#10.1.1-5#!3,10#!3.7#!10.1 xsection oval
+> modeHelix default
+> select #3.7.6
+model selected
+> select #10.1.7
+model selected
+> ~select #10.1.7
+Nothing selected
+chain B helix 6 #3.7.6 to chain B helix 7 #10.1.7: distance: 250.982Å; angle:
+.0°
+> select #3.7.7
+model selected
+> select #10.1.8
+model selected
+chain B helix 8 #10.1.8 to chain B helix 7 #3.7.7: distance: 133.997Å; angle:
+.4°
+> ~select #10.1.8
+Nothing selected
+> cartoon style #3.1-6#3.7.1-7#10.1.1-5,7-8#!3,10#!3.7#!10.1 modeHelix tube
+> sides 20
+> cartoon style #3.1-6#3.7.1-7#10.1.1-5,7-8#!3,10#!3.7#!10.1 xsection oval
+> modeHelix default
+> cartoon style #3.1-6#3.7.1-7#10.1.1-5,7-8#!3,10#!3.7#!10.1 modeHelix tube
+> sides 20
+> ui mousemode right "translate selected models"
+value: array([ 0, 150, 255, 255], dtype=uint8) default: None
+> define axis #10 perHelix true color #0096ff name test radius 0.2
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 1' centered at
+[138.89432873 118.0602333 148.78947106] with direction [-0.03321708
+-0.02481161 -0.99914014], radius 0.2, and length 21.8343
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 2' centered at
+[137.22470514 119.20230369 134.81783977] with direction [-0.01245078
+.08491942 -0.99631003], radius 0.2, and length 7.63264
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 3' centered at
+[138.05372817 108.06764281 128.51475989] with direction [ 0.8026101
+-0.59184527 0.07440569], radius 0.2, and length 18.5767
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 4' centered at
+[145.72161104 116.33145977 124.84189419] with direction [0.1508822 0.53938742
+.8284297 ], radius 0.2, and length 16.9619
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 5' centered at
+[150.81669695 129.65128059 147.93503227] with direction [0.22863824 0.50193185
+.83413966], radius 0.2, and length 38.3494
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 6' centered at
+[155.28565702 143.07274943 150.93031609] with direction [0.52188408 0.82517202
+.21616696], radius 0.2, and length 6.46639
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 7' centered at
+[161.4682541 142.4935721 136.67182626] with direction [ 0.20901679 -0.00098958
+-0.97791155], radius 0.2, and length 21.903
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 8' centered at
+[167.8756954 139.366525 144.05325253] with direction [0.21956307 0.43124242
+.87511258], radius 0.2, and length 36.8449
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 9' centered at
+[160.91926351 150.94322402 144.77402766] with direction [-0.05428096
+.15150463 -0.98696501], radius 0.2, and length 38.4235
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 10' centered at
+[153.16255893 144.72955059 127.98594293] with direction [-0.39611073
+-0.47095447 0.7882247 ], radius 0.2, and length 12.3565
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 11' centered at
+[159.05351081 123.17544409 145.89835395] with direction [0.04832853 0.00678212
+.99880847], radius 0.2, and length 30.5075
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 12' centered at
+[156.62467727 129.23983617 166.64295286] with direction [-0.60476875
+.72433613 0.33104672], radius 0.2, and length 5.7345
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 13' centered at
+[157.41472133 133.74646525 168.35308858] with direction [ 0.28281302
+-0.91915742 0.27416498], radius 0.2, and length 5.7588
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 14' centered at
+[163.09860358 136.86333389 175.22680129] with direction [ 0.34520149
+-0.79444064 0.49969992], radius 0.2, and length 10.8468
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 15' centered at
+[161.69075667 133.55055861 150.55871106] with direction [-0.36743289
+-0.02621678 -0.92968046], radius 0.2, and length 32.6292
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 16' centered at
+[141.58698056 132.34284382 157.58710316] with direction [-0.29675497 -0.608367
+.73608836], radius 0.2, and length 15.2808
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 17' centered at
+[143.12102326 127.70175984 146.94348142] with direction [-0.3506446 0.18488988
+-0.9180763 ], radius 0.2, and length 37.8351
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 18' centered at
+[138.4415738 140.61248037 144.71229819] with direction [-0.44904978 0.15017058
+.88079685], radius 0.2, and length 22.7906
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 1' centered at
+[163.29064596 182.64512887 148.75598259] with direction [-0.05834301
+.00278421 0.99829271], radius 0.2, and length 21.7356
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 2' centered at
+[165.21133484 181.2794909 134.90715963] with direction [-0.06092366 0.07495203
+.99532432], radius 0.2, and length 7.38453
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 3' centered at
+[164.53561146 192.4729011 128.65578467] with direction [-0.81244329 0.5813858
+.04389144], radius 0.2, and length 18.5121
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 4' centered at
+[157.45680002 184.37817105 123.8528681 ] with direction [-0.32193823
+-0.50009725 0.80390206], radius 0.2, and length 14.3044
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 5' centered at
+[151.36637968 172.18926675 146.45943825] with direction [-0.2624205
+-0.46650916 0.84469206], radius 0.2, and length 38.9625
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 6' centered at
+[139.79168852 158.62661407 136.63319875] with direction [-0.20785876
+-0.01337435 -0.97806741], radius 0.2, and length 21.8971
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 7' centered at
+[133.6554324 161.4499327 144.85609143] with direction [-0.24901695 -0.43824913
+.86367139], radius 0.2, and length 28.8519
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 8' centered at
+[140.13677409 149.89764288 143.42844734] with direction [ 0.05595601
+-0.15755276 -0.98592396], radius 0.2, and length 35.6621
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 9' centered at
+[148.28963686 155.95675428 127.59072569] with direction [0.45002321 0.52608488
+.72160503], radius 0.2, and length 9.98349
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 10' centered at
+[150.0577348 159.38419006 133.64248285] with direction [ 0.65314182
+-0.01925877 0.75699066], radius 0.2, and length 5.7923
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 11' centered at
+[142.89437046 178.30495372 145.65238848] with direction [-0.06655957
+-0.00993754 0.99773296], radius 0.2, and length 30.3111
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 12' centered at
+[144.66131052 173.82859124 165.72848631] with direction [-0.12653854
+-0.9912196 -0.03836286], radius 0.2, and length 5.90297
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 13' centered at
+[143.98287464 167.83074192 168.24932632] with direction [-0.27621718
+.93078782 0.23945377], radius 0.2, and length 5.71805
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 14' centered at
+[138.04156465 165.70742773 175.38542078] with direction [-0.22092881
+.89691282 0.38306377], radius 0.2, and length 11.423
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 15' centered at
+[139.6405478 167.88023035 151.11277642] with direction [ 0.3546893 0.01839823
+-0.93480319], radius 0.2, and length 34.6455
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 16' centered at
+[160.210276 168.69872157 158.12497637] with direction [0.49255082 0.48463911
+.7228545 ], radius 0.2, and length 12.405
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 17' centered at
+[158.65506626 173.21794452 146.9061338 ] with direction [ 0.34973132
+-0.20483791 -0.91418239], radius 0.2, and length 37.8498
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 18' centered at
+[161.04181351 161.02595429 140.82768715] with direction [ 0.62687875
+-0.11819244 0.77009972], radius 0.2, and length 14.1207
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 1' centered at
+[168.76700144 141.7958998 185.53240035] with direction [ 0.41814452
+-0.85006236 -0.32023295], radius 0.2, and length 14.3046
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 2' centered at
+[148.24594739 127.49258116 176.58352434] with direction [ 0.94351814
+.14475109 -0.29802793], radius 0.2, and length 5.90175
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 3' centered at
+[155.45300825 125.8189693 177.34230037] with direction [ 0.94930299
+-0.28394858 -0.13489639], radius 0.2, and length 10.0409
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 4' centered at
+[151.10493761 119.20162945 182.35952123] with direction [-0.37011828
+.49951086 0.78326328], radius 0.2, and length 14.4107
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 5' centered at
+[147.40439667 123.05661258 190.19266188] with direction [-0.00875559
+-0.79589813 -0.60536725], radius 0.2, and length 5.44482
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 6' centered at
+[141.57140032 136.12936891 177.8823915 ] with direction [-0.77937561 0.4911306
+.38905578], radius 0.2, and length 5.93556
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 7' centered at
+[149.95074934 133.06815503 185.7198464 ] with direction [ 0.74252233
+-0.64996276 -0.16189194], radius 0.2, and length 18.616
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 8' centered at
+[157.89141083 124.64099433 184.3669659 ] with direction [ 0.63240665
+-0.47596771 -0.61116002], radius 0.2, and length 6.00605
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 9' centered at
+[151.32947596 133.32780545 197.91343184] with direction [ 0.71144945
+-0.68998224 0.13328237], radius 0.2, and length 24.2622
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 10' centered at
+[157.32927478 142.29031805 203.75612885] with direction [ 0.08528956
+-0.98386135 0.15729762], radius 0.2, and length 11.4332
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 11' centered at
+[167.45280133 143.21626877 209.07861051] with direction [ 0.51964799
+.85435156 -0.00702718], radius 0.2, and length 5.78006
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 12' centered at
+[165.55567951 155.12922861 205.26760417] with direction [ 0.14497464
+-0.39113787 0.90884186], radius 0.2, and length 12.0269
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 1' centered at
+[133.39473484 157.07146631 185.87999495] with direction [-0.39860215
+.88157301 -0.2528742 ], radius 0.2, and length 19.4134
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 2' centered at
+[153.07830876 173.80337272 176.46874051] with direction [-0.94017596
+-0.14546857 -0.30807153], radius 0.2, and length 6.02798
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 3' centered at
+[146.70080408 175.02852424 177.22092458] with direction [-9.91926295e-01
+.33135128e-04 -1.26815273e-01], radius 0.2, and length 7.52775
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 4' centered at
+[150.481171 182.85501584 182.3381486 ] with direction [ 0.32582667 -0.48308072
+.81269306], radius 0.2, and length 20.9936
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 5' centered at
+[160.68109744 176.30491972 183.96304867] with direction [ 0.24314391
+-0.60924617 -0.75478484], radius 0.2, and length 6.12268
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 6' centered at
+[159.7829355 165.1504365 177.91728631] with direction [ 0.80732077 -0.4232423
+.41121665], radius 0.2, and length 5.72695
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 7' centered at
+[151.26069892 168.44683323 185.62348711] with direction [-0.73463437
+.65423124 -0.17970486], radius 0.2, and length 18.5879
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 8' centered at
+[143.49635171 176.86572021 184.07650532] with direction [-0.61488979
+.45748837 -0.6423511 ], radius 0.2, and length 5.84625
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 9' centered at
+[149.7592522 168.1814334 197.81316584] with direction [-0.71101184 0.69313967
+.11840424], radius 0.2, and length 24.3445
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 10' centered at
+[143.7666456 159.45212789 203.61703639] with direction [ 0.08102842
+-0.98798961 -0.13157097], radius 0.2, and length 11.5155
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 11' centered at
+[133.80269407 159.30297004 209.29743794] with direction [-0.52713162
+-0.58705225 0.61441184], radius 0.2, and length 5.77119
+Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 12' centered at
+[135.3884304 146.52843308 205.04864675] with direction [-0.12217055 0.41913337
+.89966748], radius 0.2, and length 11.9003
+> cartoon style #3.1-6#10.2#3.7.1-7#10.1.1-5,7-8#!3,10#!3.7#!10.1 xsection
+> oval modeHelix default
+chain B helix 1 #10.2.1 to chain B helix 2 #10.2.2: distance: 1.672Å; angle:
+.4°
+> select down
+Nothing selected
+> select down
+Nothing selected
+> select down
+Nothing selected
+> select down
+Nothing selected
+> select down
+Nothing selected
+> close #10.2.1-60
+chain E helix 11 to chain E helix 12: distance: 7.725Å; angle: 68.2°
+> select #10.1.8
+model selected
+> select #3.7.7
+model selected
+chain B helix 7 #3.7.7 to chain B helix 8 #10.1.8: distance: 133.997Å; angle:
+.4°
+> ~select #3.7.7
+Nothing selected
+> select #3.7.8
+model selected
+> select #10.1.9
+model selected
+chain B helix 8 #3.7.8 to chain B helix 9 #10.1.9: distance: 286.501Å; angle:
+.5°
+> ~select #10.1.9
+Nothing selected
+> select #3.7.9
+model selected
+> select #10.1.10
+model selected
+chain B helix 9 #3.7.9 to chain B helix 10 #10.1.10: distance: 348.095Å;
+angle: 10.4°
+> ~select #10.1.10
+Nothing selected
+> select #3.7.12
+model selected
+> ~select #3.7.12
+Nothing selected
+> select #3.7.11
+model selected
+> select #10.1.11
+model selected
+> select #3.7.11
+model selected
+> ~select #3.7.11
+Nothing selected
+> select #10.1.11
+model selected
+> ~select #10.1.11
+Nothing selected
+chain B helix 11 #10.1.11 to chain B helix 11 #3.7.11: distance: 235.684Å;
+angle: 10.5°
+> select #10.1.11
+model selected
+> ~select #10.1.11
+Nothing selected
+> select #3.7.11
+model selected
+> ~select #3.7.11
+Nothing selected
+chain B helix 11 #3.7.11 to chain B helix 11 #10.1.11: distance: 235.684Å;
+angle: 10.5°
+> select #3.7.16
+model selected
+> select #10.1.15
+model selected
+chain B helix 16 #3.7.16 to chain B helix 15 #10.1.15: distance: 263.346Å;
+angle: 0.8°
+> select #10.1.16
+model selected
+> select #3.7.17
+model selected
+chain B helix 17 #3.7.17 to chain B helix 16 #10.1.16: distance: 326.486Å;
+angle: 43.0°
+> ~select #3.7.17
+Nothing selected
+> select #3.7.19
+model selected
+> select #10.1.17
+model selected
+chain B helix 17 #10.1.17 to chain B helix 19 #3.7.19: distance: 310.377Å;
+angle: 0.7°
+> ~select #10.1.17
+Nothing selected
+> select #3.7.20
+model selected
+> select #10.1.18
+model selected
+> ~select #10.1.18
+Nothing selected
+chain B helix 20 #3.7.20 to chain B helix 18 #10.1.18: distance: 235.004Å;
+angle: 0.9°
+> select #3.7.21
+model selected
+> select #10.1.19
+model selected
+chain C helix 1 #3.7.21 to chain C helix 1 #10.1.19: distance: 230.089Å;
+angle: 7.1°
+> ~select #10.1.19
+Nothing selected
+> select #10.1.20
+model selected
+> select #3.7.22
+model selected
+chain C helix 2 #3.7.22 to chain C helix 2 #10.1.20: distance: 217.796Å;
+angle: 7.6°
+> ~select #3.7.22
+Nothing selected
+> select #10.1.23
+model selected
+> select #10.1.22
+model selected
+> ~select #10.1.22
+Nothing selected
+> select #10.1.21
+model selected
+> ~select #10.1.21
+Nothing selected
+> select #3.7.23
+model selected
+> select #10.1.23
+model selected
+chain C helix 5 #10.1.23 to chain C helix 3 #3.7.23: distance: 350.237Å;
+angle: 1.7°
+> select #10.1.21
+model selected
+> ~select #10.1.21
+Nothing selected
+> select #3.7.24
+model selected
+> select #10.1.24
+model selected
+chain C helix 4 #3.7.24 to chain C helix 6 #10.1.24: distance: 242.240Å;
+angle: 2.6°
+> select #3.7.24
+model selected
+> ~select #3.7.24
+Nothing selected
+> select #3.7.25
+model selected
+> select #10.1.25
+model selected
+chain C helix 7 #10.1.25 to chain C helix 5 #3.7.25: distance: 343.916Å;
+angle: 1.2°
+> ~select #10.1.25
+Nothing selected
+> select #3.7.26
+model selected
+> select #10.1.26
+model selected
+chain C helix 6 #3.7.26 to chain C helix 8 #10.1.26: distance: 190.730Å;
+angle: 3.0°
+> ~select #10.1.26
+Nothing selected
+> select #3.7.26
+model selected
+> ~select #3.7.26
+Nothing selected
+> select #10.1.27
+model selected
+> select #3.7.26
+model selected
+> select #10.1.26
+model selected
+> select #3.7.25
+model selected
+> select #3.7.24
+model selected
+> ~select #3.7.24
+Nothing selected
+> select #10.1.27
+model selected
+> select #3.7.27
+model selected
+chain C helix 7 #3.7.27 to chain C helix 9 #10.1.27: distance: 182.312Å;
+angle: 18.3°
+> view matrix models
+> #3.7.27,1,3.4694e-17,1.3878e-17,6.0475,4.3672e-16,1,-6.9389e-17,-7.7937,-1.3878e-17,1.3878e-17,1,4.0305
+> ~select #3.7.27
+Nothing selected
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> cartoon #3.1-6#10.2#!3,10#!3.7#!10.1
+> preset cartoons/nucleotides cylinders/stubs
+Using preset: Cartoons/Nucleotides / Cylinders/Stubs
+Changed 0 atom styles
+Preset expands to these ChimeraX commands:
+    show nucleic
+    hide protein|solvent|H
+    surf hide
+    style (protein|nucleic|solvent) & @@draw_mode=0 stick
+    cartoon
+    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
+    cartoon style ~(nucleic|strand) x round
+    cartoon style (nucleic|strand) x rect
+    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
+    cartoon style nucleic x round width 1.6 thick 1.6
+    nucleotides stubs
+> preset cartoons/nucleotides ribbons/slabs
+Using preset: Cartoons/Nucleotides / Ribbons/Slabs
+Changed 0 atom styles
+Preset expands to these ChimeraX commands:
+    show nucleic
+    hide protein|solvent|H
+    surf hide
+    style (protein|nucleic|solvent) & @@draw_mode=0 stick
+    cartoon
+    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
+    cartoon style ~(nucleic|strand) x round
+    cartoon style (nucleic|strand) x rect
+    nucleotides tube/slab shape box
+> hide #!10 models
+> select #3/b
+atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
+> color (#!3 & sel) blue
+> select #3/c
+atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
+> color (#!3 & sel) cornflower blue
+> select #3/d
+atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
+> color (#!3 & sel) purple
+> select #3/e
+atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel violet
+> ~select
+Nothing selected
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> open /Users/alexandrakaragiaridi/Desktop/Pore_for_MolBC_WT_in_DDM.json
+Opened 1 Mole channels in MolBC_WT_in_DDM_chains_renamed.pdb
+> hide #!3 models
+> open
+> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_DDM_chains_renamed.pdb
+Chain information for MolBC_WT_in_DDM_chains_renamed.pdb #22
+---
+Chain | Description
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+> ui mousemode right zoom
+> close #3
+> select #22/b
+atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
+> color (#!22 & sel) blue
+> select #22/c
+atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
+> color (#!22 & sel) cornflower blue
+> select #22/d
+atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
+> color (#!22 & sel) purple
+> select #22/e
+atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel violet
+> ~select
+Nothing selected
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> hide #22
+> cartoon style width .5 thickness .5
+> set bgColor light cyan
+> cartoon style width .5 thickness .5
+> graphics silhouettes true depthJump .01
+> camera ortho
+> select #21 & @@radius<2
+atoms, 20 residues, 1 model selected
+> show protein & sel :<2.5
+> size stickRadius .4
+Changed 152134 bond radii
+> ~select
+Nothing selected
+> cartoon suppressBackboneDisplay false
+> surface #21
+> hide #21
+> color byattribute radius #21 palette puor key true
+> key puor :0.98 :2.09 :3.20 :4.32 :5.43 showTool true
+> ui mousemode right "color key"
+atoms, 332 residues, 1 surfaces, atom radius range 0.975 to 5.43
+> ui mousemode right zoom
+[Repeated 1 time(s)]
+> ui mousemode right "translate selected models"
+> ui mousemode right "color key"
+> key pos 0.282674,0.137575 size 0.30482,0.05151
+> ui mousemode right "translate selected models"
+[Repeated 1 time(s)]
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> hide #!21 models
+> hide #!21.1 models
+> hide #!22 models
+> hide #3 models
+> open /Users/alexandrakaragiaridi/Desktop/Pore_for_MolBC_WT_in_DM.json
+Opened 1 Mole channels in MolBC_WT_in_DM_chains_renamed.pdb
+> open
+> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_DM_chains_renamed.pdb
+Chain information for MolBC_WT_in_DM_chains_renamed.pdb #24
+---
+Chain | Description
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+> close #1
+> select #24/b
+atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
+> color (#!24 & sel) blue
+> select #24/c
+atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
+> color (#!24 & sel) cornflower blue
+> select #24/d
+atoms, 2035 bonds, 421 residues, 1 model selected
+> color sel purple
+> select #24/e
+atoms, 2005 bonds, 1 pseudobond, 456 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel violet
+> select add #24
+atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
+> select subtract #24
+Nothing selected
+> hide #24
+> cartoon style width .5 thickness .5
+> graphics silhouettes true depthJump .01
+> camera ortho
+> select #23 & @@radius<2
+atoms, 43 residues, 1 model selected
+> show protein & sel :<2.5
+> size stickRadius .4
+Changed 152134 bond radii
+> ~select
+Nothing selected
+> cartoon suppressBackboneDisplay false
+> surface #23
+> hide #23
+> color byattribute radius #23 palette puor key true
+> key puor :0.79 :2.33 :3.87 :5.41 :6.95 showTool true
+atoms, 367 residues, 1 surfaces, atom radius range 0.793 to 6.95
+> show #3 models
+> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
+> hide #!23 models
+> hide #!23.1 models
+> hide #!24 models
+> open /Users/alexandrakaragiaridi/Desktop/Pore_for_MolBC_WT_in_C5.json
+Opened 1 Mole channels in MolBC_WT_in_C5_chains_renamed.pdb
+> view
+> close #5
+> open
+> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_C5_chains_renamed.pdb
+Chain information for MolBC_WT_in_C5_chains_renamed.pdb #5
+---
+Chain | Description
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+> select subtract #4
+Nothing selected
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> ui mousemode right "translate selected models"
+> select #5/b
+atoms, 2405 bonds, 2 pseudobonds, 309 residues, 2 models selected
+> color (#!5 & sel) blue
+> select #5/c
+atoms, 2353 bonds, 2 pseudobonds, 303 residues, 2 models selected
+> color (#!5 & sel) cornflower blue
+> select #5/d
+atoms, 2036 bonds, 251 residues, 1 model selected
+> color sel purple
+> select #5/e
+atoms, 2044 bonds, 252 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel violet
+> hide #5
+> cartoon style width .5 thickness .5
+> select add #5
+atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
+> select subtract #5
+Nothing selected
+> cartoon style width .5 thickness .5
+> graphics silhouettes true depthJump .01
+> camera ortho
+> select #1 & @@radius<2
+atoms, 60 residues, 1 model selected
+> show protein & sel :<2.5
+> size stickRadius .4
+Changed 152134 bond radii
+> ~select
+Nothing selected
+> cartoon suppressBackboneDisplay false
+> surface #1
+> hide #1
+> color byattribute radius #1 palette puor
+atoms, 287 residues, 1 surfaces, atom radius range 0.869 to 6.09
+> color byattribute radius #1 palette puor key true
+> key puor :0.87 :2.17 :3.48 :4.79 :6.09 showTool true
+atoms, 287 residues, 1 surfaces, atom radius range 0.869 to 6.09
+> ui mousemode right "rotate selected models"
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> hide #!5 models
+> hide #!1 models
+> hide #!1.1 models
+> open /Users/alexandrakaragiaridi/Desktop/Pore_for_MolABC_WT_in_DDM.json
+Opened 1 Mole channels in MolABC_no_nuc.pdb
+> open
+> /Users/alexandrakaragiaridi/Desktop/MolABC_no_nuc_everything/MolABC_no_nuc.pdb
+Chain information for MolABC_no_nuc.pdb #26
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+> view
+> close #7
+> hide #25.1#!26 atoms
+> show #25.1#!26 cartoons
+> show #25.1#!26 atoms
+> select add #26
+atoms, 11571 bonds, 1 pseudobond, 1452 residues, 2 models selected
+> hide sel atoms
+> select subtract #26
+Nothing selected
+> select subtract #4
+Nothing selected
+> ui mousemode right "translate selected models"
+> select #26/a
+atoms, 2532 bonds, 1 pseudobond, 313 residues, 2 models selected
+> color (#!26 & sel) orange
+> select #26/
+Expected an objects specifier or a keyword
+> select #26/b
+atoms, 2496 bonds, 320 residues, 1 model selected
+> color sel blue
+> select #26/c
+atoms, 2465 bonds, 316 residues, 1 model selected
+> color sel cornflower blue
+> select #26/d
+atoms, 2043 bonds, 252 residues, 1 model selected
+> color sel purple
+> select #26/e
+atoms, 2035 bonds, 251 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel violet
+> ~select
+Nothing selected
+> hide #26
+> cartoon style width .5 thickness .5
+> graphics silhouettes true depthJump .01
+> camera ortho
+> select #25 & @@radius<2
+atoms, 22 residues, 1 model selected
+> show protein & sel :<2.5
+> size stickRadius .4
+Changed 152134 bond radii
+> ~select
+Nothing selected
+> cartoon suppressBackboneDisplay false
+> surface #25
+> hide #25
+> color byattribute radius #25 palette puor
+atoms, 325 residues, 1 surfaces, atom radius range 0.987 to 4.92
+> color byattribute radius #25 palette puor key true
+> key puor :0.99 :1.97 :2.96 :3.94 :4.92 showTool true
+atoms, 325 residues, 1 surfaces, atom radius range 0.987 to 4.92
+> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
+> hide #!25 models
+> hide #!25.1 models
+> hide #!26 models
+> open
+> /Users/alexandrakaragiaridi/Desktop/Pore_for_MolABC_E154Q_AMPPNP_in_DDM.json
+Traceback (most recent call last):
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/open_command/dialog.py", line 162, in _qt_safe
+run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/core/commands/run.py", line 38, in run
+results = command.run(text, log=log, return_json=return_json)
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/core/commands/cli.py", line 2897, in run
+result = ci.function(session, **kw_args)
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/open_command/cmd.py", line 119, in cmd_open
+models = Command(session, registry=registry).run(provider_cmd_text,
+log=log)[0]
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/core/commands/cli.py", line 2897, in run
+result = ci.function(session, **kw_args)
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/open_command/cmd.py", line 194, in provider_open
+models, status = collated_open(session, None, [data], data_format,
+_add_models,
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/open_command/cmd.py", line 464, in collated_open
+return remember_data_format()
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
+models, status = func(*func_args, **func_kw)
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/mole/__init__.py", line 27, in open
+return mole.read_mole_json(session, data, file_name, **kw)
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/mole/mole.py", line 44, in read_mole_json
+models = channel_models(session, j['Channels'], transparency/100.0)
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/mole/mole.py", line 83, in channel_models
+ms.create_marker((x,y,z), color, r)
+File
+"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
+packages/chimerax/markers/markers.py", line 26, in create_marker
+a.radius = radius
+File "atomic_cpp/cymol.pyx", line 456, in
+chimerax.atomic.cymol.CyAtom.radius.__set__
+RuntimeError: radius must be positive
+RuntimeError: radius must be positive
+File "atomic_cpp/cymol.pyx", line 456, in
+chimerax.atomic.cymol.CyAtom.radius.__set__
+See log for complete Python traceback.
+> open
+> /Users/alexandrakaragiaridi/Desktop/Pore_for_MolABC_E154Q_AMPPNP_in_DDM_MolA_deleted.json
+Opened 1 Mole channels in MolABC_nuc_MolA_deleted.pdb
+> open "/Users/alexandrakaragiaridi/Desktop/MolABC_nuc_everything/yes
+> SBP/MolABC_nuc_MolA_deleted.pdb"
+Chain information for MolABC_nuc_MolA_deleted.pdb #27
+---
+Chain | Description
+B | No description available
+C | No description available
+D E | No description available
+> close #12
+> ui mousemode right "rotate selected models"
+> ui mousemode right "translate selected models"
+> select #27/b
+atoms, 2327 bonds, 1 pseudobond, 299 residues, 2 models selected
+> color (#!27 & sel) blue
+> select #27/c
+atoms, 2550 bonds, 326 residues, 1 model selected
+> color sel cornflower blue
+> select #27/d
+atoms, 2035 bonds, 251 residues, 1 model selected
+> color sel purple
+> select #27/e
+atoms, 2035 bonds, 251 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel violet
+> ui hideFloating toggle
+> ~select
+Nothing selected
+> select ::name="ANP"
+atoms, 184 bonds, 4 residues, 2 models selected
+> color (#!27 & sel) forest green
+> ~select
+Nothing selected
+> hide #27
+> show #27
+> hide #7.1#!27 atoms
+> select ::name="ANP"
+atoms, 184 bonds, 4 residues, 2 models selected
+> show sel & #!27 atoms
+> ~select
+Nothing selected
+> cartoon style width .5 thickness .5
+> graphics silhouettes true depthJump .01
+> camera ortho
+> select #7 & @@radius<2
+atoms, 88 residues, 1 model selected
+> show sel atoms
+> close #7
+> open
+> /Users/alexandrakaragiaridi/Desktop/Pore_for_MolABC_E154Q_AMPPNP_in_DDM_MolA_deleted.json
+Opened 1 Mole channels in MolABC_nuc_MolA_deleted.pdb
+[deleted to fit within ticket limits]
 > select #7 & @@radius<2